From b92ede79ea7ac7680104c382b5b382001c3ab25b Mon Sep 17 00:00:00 2001
From: jlmaier <jlmaier@ncsu.edu>
Date: Thu, 2 Jan 2025 16:06:40 -0500
Subject: [PATCH] github page updates

---
 404.html                                  |   2 +-
 apple-touch-icon.png                      | Bin 9128 -> 6725 bytes
 articles/TrIdent-vignette.html            | 128 +++++++++++-----------
 articles/index.html                       |   2 +-
 authors.html                              |  12 +-
 favicon-96x96.png                         | Bin 3864 -> 2793 bytes
 favicon.ico                               | Bin 15086 -> 15086 bytes
 favicon.svg                               |   2 +-
 index.html                                | 114 +++++++++++++------
 logo.png                                  | Bin 10640 -> 5399 bytes
 news/index.html                           |  28 ++++-
 pkgdown.yml                               |   2 +-
 reference/NARemover.html                  |   4 +-
 reference/TrIdent-package.html            |   2 +-
 reference/TrIdentClassifier.html          |  37 +++++--
 reference/TrIdentSampleOutput.html        |  21 +++-
 reference/VLPFractionSamplePileup.html    |   4 +-
 reference/VLPtoWCRatioCalc.html           |   4 +-
 reference/WholeCommunitySamplePileup.html |   4 +-
 reference/allPatternMatches.html          |   4 +-
 reference/allProphageLikeClassifs.html    |   4 +-
 reference/allSlopingClassifs.html         |   4 +-
 reference/blockBuilder.html               |   4 +-
 reference/blockTranslator.html            |   4 +-
 reference/changeSlope.html                |   4 +-
 reference/changeSlopeWStart.html          |   4 +-
 reference/changeWindowSize.html           |   4 +-
 reference/contigClassSumm.html            |   4 +-
 reference/figures/README-example-1.png    | Bin 9573 -> 12407 bytes
 reference/figures/README-example-10.png   | Bin 0 -> 9919 bytes
 reference/figures/README-example-11.png   | Bin 0 -> 9834 bytes
 reference/figures/README-example-12.png   | Bin 0 -> 9605 bytes
 reference/figures/README-example-13.png   | Bin 0 -> 9605 bytes
 reference/figures/README-example-2.png    | Bin 0 -> 11691 bytes
 reference/figures/README-example-3.png    | Bin 0 -> 10959 bytes
 reference/figures/README-example-4.png    | Bin 0 -> 12074 bytes
 reference/figures/README-example-5.png    | Bin 0 -> 12079 bytes
 reference/figures/README-example-6.png    | Bin 0 -> 11549 bytes
 reference/figures/README-example-7.png    | Bin 0 -> 12012 bytes
 reference/figures/README-example-8.png    | Bin 0 -> 10905 bytes
 reference/figures/README-example-9.png    | Bin 0 -> 9879 bytes
 reference/figures/logo.png                | Bin 10640 -> 5399 bytes
 reference/fullSlope.html                  |   4 +-
 reference/index.html                      |   2 +-
 reference/leftRightBlockTranslater.html   |   4 +-
 reference/makeBlockPattern.html           |   4 +-
 reference/makeFullSlopes.html             |   4 +-
 reference/makeSlopesWStarts.html          |   4 +-
 reference/noPattern.html                  |   2 +-
 reference/patternBuilder.html             |   4 +-
 reference/patternMatchSize.html           |  11 +-
 reference/patternMatcher.html             |   2 +-
 reference/pileupFormatter.html            |   4 +-
 reference/plotTrIdentResults.html         |  30 ++++-
 reference/prophageLikeBorders.html        |   4 +-
 reference/prophageLikeElevation.html      |  12 +-
 reference/prophageLikeZoom.html           |   4 +-
 reference/resultsHisto.html               |   2 +-
 reference/slopeSumm.html                  |   4 +-
 reference/slopeTranslator.html            |   4 +-
 reference/slopeWithStart.html             |   4 +-
 reference/specTransductionPlot.html       |   4 +-
 reference/specTransductionSearch.html     |   4 +-
 reference/specializedTransductionID.html  |  22 +++-
 reference/zeroCountSearch.html            |   4 +-
 search.json                               |   2 +-
 site.webmanifest                          |  21 ++++
 web-app-manifest-192x192.png              | Bin 10035 -> 7299 bytes
 web-app-manifest-512x512.png              | Bin 53713 -> 38169 bytes
 69 files changed, 372 insertions(+), 196 deletions(-)
 create mode 100644 reference/figures/README-example-10.png
 create mode 100644 reference/figures/README-example-11.png
 create mode 100644 reference/figures/README-example-12.png
 create mode 100644 reference/figures/README-example-13.png
 create mode 100644 reference/figures/README-example-2.png
 create mode 100644 reference/figures/README-example-3.png
 create mode 100644 reference/figures/README-example-4.png
 create mode 100644 reference/figures/README-example-5.png
 create mode 100644 reference/figures/README-example-6.png
 create mode 100644 reference/figures/README-example-7.png
 create mode 100644 reference/figures/README-example-8.png
 create mode 100644 reference/figures/README-example-9.png
 create mode 100644 site.webmanifest

diff --git a/404.html b/404.html
index 00e4482..f9c9132 100644
--- a/404.html
+++ b/404.html
@@ -27,7 +27,7 @@
 
     <a class="navbar-brand me-2" href="https://jlmaier12.github.io/TrIdent/index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/apple-touch-icon.png b/apple-touch-icon.png
index 6b9711f6403d2b449b0067102696524c0ace75f6..599b687ebc04e6e9459f09a84fcdb85e0a9642f6 100644
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diff --git a/articles/TrIdent-vignette.html b/articles/TrIdent-vignette.html
index c47c6e9..bbf86ec 100644
--- a/articles/TrIdent-vignette.html
+++ b/articles/TrIdent-vignette.html
@@ -31,7 +31,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -117,45 +117,25 @@ <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#i
 transduced DNA in pure cultures and microbial communities. Microbiome 8,
 158 (2020). <a href="https://doi.org/10.1186/s40168-020-00935-5" class="external-link uri">https://doi.org/10.1186/s40168-020-00935-5</a></p>
 <div class="section level3">
-<h3 id="acknowledgments">Acknowledgments<a class="anchor" aria-label="anchor" href="#acknowledgments"></a>
+<h3 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a>
 </h3>
-<p>TrIdent is the result of the combined effort and brain power of many
-individuals. Specifically, we would like to thank Dr. Manuel Kleiner,
-Dr. Ben Callahan, Dr. Breck Duerkop and Dr. Craig Gin for their
-individual expertise and overall support!</p>
 </div>
 <div class="section level3">
-<h3 id="funding">Funding<a class="anchor" aria-label="anchor" href="#funding"></a>
-</h3>
-<p>The development of TrIdent was supported by a seed grant from the
-North Carolina State University Data Science Academy and by the National
-Institutes of Health under Award Numbers R35GM138362 and
-R01Al171046.</p>
-</div>
-</div>
-<div class="section level2">
-<h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a>
-</h2>
-<div class="section level3">
-<h3 id="cran-install">CRAN install<a class="anchor" aria-label="anchor" href="#cran-install"></a>
+<h3 id="bioconductor-install">Bioconductor install<a class="anchor" aria-label="anchor" href="#bioconductor-install"></a>
 </h3>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://pak.r-lib.org/" class="external-link">"pak"</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span>
-<span>  <span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"pak"</span><span class="op">)</span></span>
+<code class="sourceCode R"><span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://bioconductor.github.io/BiocManager/" class="external-link">"BiocManager"</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span>
+<span>  <span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"BiocManager"</span><span class="op">)</span></span>
 <span><span class="op">}</span></span>
 <span></span>
-<span><span class="fu">pak</span><span class="fu">::</span><span class="fu">pak</span><span class="op">(</span><span class="st">"jlmaier12/TrIdent"</span><span class="op">)</span></span>
+<span><span class="fu">BiocManager</span><span class="fu">::</span><span class="fu"><a href="https://bioconductor.github.io/BiocManager/reference/install.html" class="external-link">install</a></span><span class="op">(</span><span class="st">"TrIdent"</span><span class="op">)</span></span>
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/jlmaier12/TrIdent" class="external-link">TrIdent</a></span><span class="op">)</span></span></code></pre></div>
 </div>
 <div class="section level3">
 <h3 id="github-install">GitHub install<a class="anchor" aria-label="anchor" href="#github-install"></a>
 </h3>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://devtools.r-lib.org/" class="external-link">"devtools"</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span>
-<span>  <span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"devtools"</span><span class="op">)</span></span>
-<span><span class="op">}</span></span>
-<span></span>
-<span><span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"jlmaier12/TrIdent"</span><span class="op">)</span></span>
+<code class="sourceCode R"><span><span class="fu">BiocManager</span><span class="fu">::</span><span class="fu"><a href="https://bioconductor.github.io/BiocManager/reference/install.html" class="external-link">install</a></span><span class="op">(</span><span class="st">"jlmaier12/TrIdent"</span><span class="op">)</span></span>
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/jlmaier12/TrIdent" class="external-link">TrIdent</a></span><span class="op">)</span></span></code></pre></div>
 </div>
 </div>
@@ -558,9 +538,9 @@ <h3 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a>
 <span><span class="co">#&gt; Almost done with pattern-matching!</span></span>
 <span><span class="co">#&gt; Determining sizes (bp) of pattern matches</span></span>
 <span><span class="co">#&gt; Identifying highly active/abundant or heterogenously integrated</span></span>
-<span><span class="co">#&gt;         Prophage-like elements</span></span>
+<span><span class="co">#&gt;       Prophage-like elements</span></span>
 <span><span class="co">#&gt; Finalizing output</span></span>
-<span><span class="co">#&gt; Execution time: 14.75secs</span></span>
+<span><span class="co">#&gt; Execution time: 24.25secs</span></span>
 <span><span class="co">#&gt; 1 contigs were filtered out based on low read coverage</span></span>
 <span><span class="co">#&gt; 0 contigs were filtered out based on length</span></span>
 <span><span class="co">#&gt; </span></span>
@@ -569,7 +549,6 @@ <h3 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a>
 <span><span class="co">#&gt; 3 of the prophage-like classifications are highly active or abundant</span></span>
 <span><span class="co">#&gt; 1 of the prophage-like classifications are mixed, i.e. heterogenously</span></span>
 <span><span class="co">#&gt;         integrated into their bacterial host population</span></span></code></pre></div>
-<p><img src="TrIdent-vignette_files/figure-html/unnamed-chunk-8-1.png" width="100%"></p>
 </div>
 <div class="section level3">
 <h3 id="argumentsparameters">Arguments/Parameters<a class="anchor" aria-label="anchor" href="#argumentsparameters"></a>
@@ -578,7 +557,7 @@ <h3 id="argumentsparameters">Arguments/Parameters<a class="anchor" aria-label="a
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/TrIdentClassifier.html">TrIdentClassifier</a></span><span class="op">(</span><span class="va">VLPpileup</span>, <span class="va">WCpileup</span>,</span>
 <span>  windowSize <span class="op">=</span> <span class="fl">1000</span>, minBlockSize <span class="op">=</span> <span class="fl">10000</span>,</span>
 <span>  maxBlockSize <span class="op">=</span> <span class="cn">Inf</span>, minContigLength <span class="op">=</span> <span class="fl">30000</span>, minSlope <span class="op">=</span> <span class="fl">0.001</span>,</span>
-<span>  suggFiltThresh <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">SaveFilesTo</span></span>
+<span>  suggFiltThresh <span class="op">=</span> <span class="cn">FALSE</span>, verbose <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">SaveFilesTo</span></span>
 <span><span class="op">)</span></span></code></pre></div>
 <ul>
 <li>
@@ -609,6 +588,9 @@ <h3 id="argumentsparameters">Arguments/Parameters<a class="anchor" aria-label="a
 threshold for TrIdent classifications based on the normalized
 pattern-match scores. Default is FALSE.</li>
 <li>
+<code>verbose</code>: TRUE or FALSE. Print progress messages to
+console. Default is TRUE.</li>
+<li>
 <code>SaveFilesTo</code>: Optional, Provide a path to the directory
 you wish to save output to. A folder will be made within the provided
 directory to store results.</li>
@@ -617,13 +599,6 @@ <h3 id="argumentsparameters">Arguments/Parameters<a class="anchor" aria-label="a
 <div class="section level3">
 <h3 id="output">Output<a class="anchor" aria-label="anchor" href="#output"></a>
 </h3>
-<p><code><a href="../reference/TrIdentClassifier.html">TrIdentClassifier()</a></code> outputs a histogram displaying the
-overall abundance and quality of pattern-matches in addition to the
-composition of classifications. The displayed pattern-match scores are
-normalized by dividing each score by its associated contig length. The
-scores are normalized to visualize the overall quality of
-pattern-matching for the entire dataset. Remember, smaller pattern-match
-scores correspond to better pattern-matches.</p>
 <p>The output of <code><a href="../reference/TrIdentClassifier.html">TrIdentClassifier()</a></code> is a list containing
 five objects:</p>
 <ol style="list-style-type: decimal">
@@ -637,6 +612,13 @@ <h3 id="output">Output<a class="anchor" aria-label="anchor" href="#output"></a>
 <li>FilteredOutContigTable: A table containing contigs that were
 filtered out and the reason why (low read coverage or too short).</li>
 <li>windowSize: The <code>windowSize</code> used.</li>
+<li>ResultHistogram: a histogram displaying the overall abundance and
+quality of pattern-matches in addition to the composition of
+classifications. The displayed pattern-match scores are normalized by
+dividing each score by its associated contig length. The scores are
+normalized to visualize the overall quality of pattern-matching for the
+entire dataset. Remember, smaller pattern-match scores correspond to
+better pattern-matches.</li>
 </ol>
 <p>Save the desired list-item to a new variable using its associated
 name.</p>
@@ -1169,7 +1151,7 @@ <h3 id="argumentsparameters-2">Arguments/Parameters<a class="anchor" aria-label=
 <div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/specializedTransductionID.html">specializedTransductionID</a></span><span class="op">(</span><span class="va">VLPpileup</span>, <span class="va">TrIdentResults</span>,</span>
 <span>  noReadCov <span class="op">=</span> <span class="fl">500</span>, specTransLength <span class="op">=</span> <span class="fl">2000</span>,</span>
-<span>  logScale <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">matchScoreFilter</span>,</span>
+<span>  logScale <span class="op">=</span> <span class="cn">FALSE</span>, verbose <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">matchScoreFilter</span>,</span>
 <span>  <span class="va">SaveFilesTo</span>, <span class="va">specificContig</span></span>
 <span><span class="op">)</span></span></code></pre></div>
 <ul>
@@ -1185,11 +1167,7 @@ <h3 id="argumentsparameters-2">Arguments/Parameters<a class="anchor" aria-label=
 <li>
 <code>specTransLength</code>: Number of basepairs of non-zero read
 coverage needed for specialized transduction to be considered. Default
-is 2000. Must be at least</li>
-</ul>
-<ol start="100" style="list-style-type: decimal"><li>
-</li></ol>
-<ul>
+is 2000. Must be at least 100.</li>
 <li>
 <code>logScale</code>: TRUE or FALSE, display VLP-fraction read
 coverage in log10 scale. Default is FALSE.</li>
@@ -1199,6 +1177,9 @@ <h3 id="argumentsparameters-2">Arguments/Parameters<a class="anchor" aria-label=
 provided by <code><a href="../reference/TrIdentClassifier.html">TrIdentClassifier()</a></code> if
 <code>suggFiltThresh=TRUE</code>.</li>
 <li>
+<code>verbose</code>: TRUE or FALSE. Print progress messages to
+console. Default is TRUE.</li>
+<li>
 <code>SaveFilesTo</code>: Optional, Provide a path to the directory
 you wish to save output to. A folder will be made within the provided
 directory to store results.</li>
@@ -1832,8 +1813,27 @@ <h2 id="generate-final-trident-summary-table">Generate final TrIdent summary tab
 </table>
 </div>
 <div class="section level2">
-<h2 id="session-information">Session Information<a class="anchor" aria-label="anchor" href="#session-information"></a>
+<h2 id="supplemental-information">Supplemental information<a class="anchor" aria-label="anchor" href="#supplemental-information"></a>
 </h2>
+<div class="section level3">
+<h3 id="acknowledgments">Acknowledgments<a class="anchor" aria-label="anchor" href="#acknowledgments"></a>
+</h3>
+<p>TrIdent is the result of the combined effort and brain power of many
+individuals. Specifically, we would like to thank Dr. Manuel Kleiner,
+Dr. Ben Callahan, Dr. Breck Duerkop and Dr. Craig Gin for their
+individual expertise and overall support!</p>
+</div>
+<div class="section level3">
+<h3 id="funding">Funding<a class="anchor" aria-label="anchor" href="#funding"></a>
+</h3>
+<p>The development of TrIdent was supported by a seed grant from the
+North Carolina State University Data Science Academy and by the National
+Institutes of Health under Award Numbers R35GM138362 and
+R01Al171046.</p>
+</div>
+<div class="section level3">
+<h3 id="session-information">Session Information<a class="anchor" aria-label="anchor" href="#session-information"></a>
+</h3>
 <div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/sessionInfo.html" class="external-link">sessionInfo</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="co">#&gt; R version 4.2.1 (2022-06-23 ucrt)</span></span>
@@ -1853,24 +1853,30 @@ <h2 id="session-information">Session Information<a class="anchor" aria-label="an
 <span><span class="co">#&gt; [1] stats     graphics  grDevices utils     datasets  methods   base     </span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; other attached packages:</span></span>
-<span><span class="co">#&gt; [1] kableExtra_1.4.0   ggplot2_3.5.1      patchwork_1.3.0    knitr_1.49        </span></span>
-<span><span class="co">#&gt; [5] TrIdent_0.0.0.9000</span></span>
+<span><span class="co">#&gt; [1] kableExtra_1.4.0 ggplot2_3.5.1    patchwork_1.3.0  knitr_1.49      </span></span>
+<span><span class="co">#&gt; [5] TrIdent_0.99.2   BiocStyle_2.26.0</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; loaded via a namespace (and not attached):</span></span>
-<span><span class="co">#&gt;  [1] Rcpp_1.0.13-1      bslib_0.8.0        compiler_4.2.1     pillar_1.9.0      </span></span>
-<span><span class="co">#&gt;  [5] jquerylib_0.1.4    tools_4.2.1        digest_0.6.37      viridisLite_0.4.2 </span></span>
-<span><span class="co">#&gt;  [9] jsonlite_1.8.9     evaluate_1.0.1     lifecycle_1.0.4    tibble_3.2.1      </span></span>
-<span><span class="co">#&gt; [13] gtable_0.3.6       pkgconfig_2.0.3    rlang_1.1.4        cli_3.6.2         </span></span>
-<span><span class="co">#&gt; [17] rstudioapi_0.17.1  roll_1.1.7         yaml_2.3.10        pkgdown_2.1.1     </span></span>
-<span><span class="co">#&gt; [21] xfun_0.49          fastmap_1.2.0      xml2_1.3.6         withr_3.0.2       </span></span>
-<span><span class="co">#&gt; [25] stringr_1.5.1      dplyr_1.1.4        generics_0.1.3     desc_1.4.3        </span></span>
-<span><span class="co">#&gt; [29] fs_1.6.5           vctrs_0.6.5        htmlwidgets_1.6.4  sass_0.4.9        </span></span>
-<span><span class="co">#&gt; [33] systemfonts_1.1.0  grid_4.2.1         tidyselect_1.2.1   svglite_2.1.3     </span></span>
-<span><span class="co">#&gt; [37] glue_1.8.0         R6_2.5.1           textshaping_0.4.1  fansi_1.0.6       </span></span>
-<span><span class="co">#&gt; [41] rmarkdown_2.29     purrr_1.0.2        tidyr_1.3.1        farver_2.1.2      </span></span>
-<span><span class="co">#&gt; [45] magrittr_2.0.3     scales_1.3.0       htmltools_0.5.8.1  colorspace_2.1-1  </span></span>
-<span><span class="co">#&gt; [49] labeling_0.4.3     ragg_1.3.3         utf8_1.2.4         stringi_1.8.4     </span></span>
-<span><span class="co">#&gt; [53] RcppParallel_5.1.9 munsell_0.5.1      cachem_1.1.0</span></span></code></pre></div>
+<span><span class="co">#&gt;  [1] tidyselect_1.2.1    xfun_0.49           bslib_0.8.0        </span></span>
+<span><span class="co">#&gt;  [4] purrr_1.0.2         colorspace_2.1-1    vctrs_0.6.5        </span></span>
+<span><span class="co">#&gt;  [7] generics_0.1.3      htmltools_0.5.8.1   viridisLite_0.4.2  </span></span>
+<span><span class="co">#&gt; [10] yaml_2.3.10         utf8_1.2.4          rlang_1.1.4        </span></span>
+<span><span class="co">#&gt; [13] pkgdown_2.1.1       jquerylib_0.1.4     pillar_1.9.0       </span></span>
+<span><span class="co">#&gt; [16] glue_1.8.0          withr_3.0.2         lifecycle_1.0.4    </span></span>
+<span><span class="co">#&gt; [19] stringr_1.5.1       munsell_0.5.1       gtable_0.3.6       </span></span>
+<span><span class="co">#&gt; [22] ragg_1.3.3          htmlwidgets_1.6.4   evaluate_1.0.1     </span></span>
+<span><span class="co">#&gt; [25] labeling_0.4.3      fastmap_1.2.0       fansi_1.0.6        </span></span>
+<span><span class="co">#&gt; [28] Rcpp_1.0.13-1       scales_1.3.0        BiocManager_1.30.25</span></span>
+<span><span class="co">#&gt; [31] cachem_1.1.0        desc_1.4.3          RcppParallel_5.1.9 </span></span>
+<span><span class="co">#&gt; [34] jsonlite_1.8.9      farver_2.1.2        systemfonts_1.1.0  </span></span>
+<span><span class="co">#&gt; [37] fs_1.6.5            textshaping_0.4.1   digest_0.6.37      </span></span>
+<span><span class="co">#&gt; [40] stringi_1.8.4       bookdown_0.41       dplyr_1.1.4        </span></span>
+<span><span class="co">#&gt; [43] roll_1.1.7          grid_4.2.1          cli_3.6.2          </span></span>
+<span><span class="co">#&gt; [46] tools_4.2.1         magrittr_2.0.3      sass_0.4.9         </span></span>
+<span><span class="co">#&gt; [49] tibble_3.2.1        tidyr_1.3.1         pkgconfig_2.0.3    </span></span>
+<span><span class="co">#&gt; [52] xml2_1.3.6          rmarkdown_2.29      svglite_2.1.3      </span></span>
+<span><span class="co">#&gt; [55] rstudioapi_0.17.1   R6_2.5.1            compiler_4.2.1</span></span></code></pre></div>
+</div>
 </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
     </nav></aside>
diff --git a/articles/index.html b/articles/index.html
index c37eab0..525dcc3 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/authors.html b/authors.html
index f617be8..e28fcb4 100644
--- a/authors.html
+++ b/authors.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -38,7 +38,7 @@
       <h2>Authors</h2>
 
       <ul class="list-unstyled"><li>
-          <p><strong>Jessie Maier</strong>. Author, maintainer, copyright holder. <a href="https://orcid.org/0009-0001-8575-5386" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
+          <p><strong>Jessie Maier</strong>. Author, maintainer. <a href="https://orcid.org/0009-0001-8575-5386" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
           </p>
         </li>
         <li>
@@ -63,14 +63,14 @@ <h2>Authors</h2>
       <h2 id="citation">Citation</h2>
       <p><small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/DESCRIPTION" class="external-link"><code>DESCRIPTION</code></a></small></p>
 
-      <p>Maier J, Rabasco J, Gin C, Callahan B, Kleiner M (2024).
-<em>TrIdent: Detect Genetic Transduction Events in Metagenomes using Read Coverage Pattern-Matching</em>.
+      <p>Maier J, Rabasco J, Gin C, Callahan B, Kleiner M (2025).
+<em>TrIdent: TrIdent - Transduction Identification</em>.
 https://github.com/jlmaier12/TrIdent, https://jlmaier12.github.io/TrIdent/.
 </p>
       <pre>@Manual{,
-  title = {TrIdent: Detect Genetic Transduction Events in Metagenomes using Read Coverage Pattern-Matching},
+  title = {TrIdent: TrIdent - Transduction Identification},
   author = {Jessie Maier and Jorden Rabasco and Craig Gin and Benjamin Callahan and Manuel Kleiner},
-  year = {2024},
+  year = {2025},
   note = {https://github.com/jlmaier12/TrIdent, https://jlmaier12.github.io/TrIdent/},
 }</pre>
     </div>
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diff --git a/index.html b/index.html
index 4e66c18..53f47c8 100644
--- a/index.html
+++ b/index.html
@@ -5,7 +5,7 @@
 <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
-<title>Detect Genetic Transduction Events in Metagenomes using Read Coverage Pattern-Matching • TrIdent</title>
+<title>TrIdent - Transduction Identification • TrIdent</title>
 <!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png">
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 <link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png">
@@ -16,9 +16,9 @@
 <link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
 <script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet">
 <link href="deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet">
-<script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Detect Genetic Transduction Events in Metagenomes using Read Coverage Pattern-Matching">
-<meta name="description" content="`TrIdent` automates the analysis of transductomics data by detecting, classifying, and characterizing read coverage patterns associated with potential transduction events. Transductomics is a DNA sequencing-based method for the detection and characterization of transduction events in pure cultures and complex communities. Transductomics relies on mapping sequencing reads from a viral-like particle (VLP)-fraction of a sample to contigs assembled from the metagenome (whole-community) of the same sample. Reads from bacterial DNA carried by VLPs will map back to the bacterial contigs of origin creating read coverage patterns indicative of ongoing transduction.">
-<meta property="og:description" content="`TrIdent` automates the analysis of transductomics data by detecting, classifying, and characterizing read coverage patterns associated with potential transduction events. Transductomics is a DNA sequencing-based method for the detection and characterization of transduction events in pure cultures and complex communities. Transductomics relies on mapping sequencing reads from a viral-like particle (VLP)-fraction of a sample to contigs assembled from the metagenome (whole-community) of the same sample. Reads from bacterial DNA carried by VLPs will map back to the bacterial contigs of origin creating read coverage patterns indicative of ongoing transduction.">
+<script src="deps/headroom-0.11.0/headroom.min.js"></script><script src="deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="deps/search-1.0.0/fuse.min.js"></script><script src="deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="TrIdent - Transduction Identification">
+<meta name="description" content="The `TrIdent` R package automates the analysis of transductomics data by detecting, classifying, and characterizing read coverage patterns associated with potential transduction events. Transductomics is a DNA sequencing-based method for the detection and characterization of transduction events in pure cultures and complex communities. Transductomics relies on mapping sequencing reads from a viral-like particle (VLP)-fraction of a sample to contigs assembled from the metagenome (whole-community) of the same sample. Reads from bacterial DNA carried by VLPs will map back to the bacterial contigs of origin creating read coverage patterns indicative of ongoing transduction.">
+<meta property="og:description" content="The `TrIdent` R package automates the analysis of transductomics data by detecting, classifying, and characterizing read coverage patterns associated with potential transduction events. Transductomics is a DNA sequencing-based method for the detection and characterization of transduction events in pure cultures and complex communities. Transductomics relies on mapping sequencing reads from a viral-like particle (VLP)-fraction of a sample to contigs assembled from the metagenome (whole-community) of the same sample. Reads from bacterial DNA carried by VLPs will map back to the bacterial contigs of origin creating read coverage patterns indicative of ongoing transduction.">
 <meta property="og:image" content="https://jlmaier12.github.io/TrIdent/logo.png">
 </head>
 <body>
@@ -29,7 +29,7 @@
 
     <a class="navbar-brand me-2" href="index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -64,10 +64,8 @@
 <img src="logo.png" class="logo" alt=""><h1 id="trident">TrIdent<a class="anchor" aria-label="anchor" href="#trident"></a>
 </h1>
 </div>
-<!-- badges: start -->
-<!-- badges: end -->
-
-<p>TrIdent automates the analysis of transductomics data by detecting, classifying, and characterizing read coverage patterns associated with potential transduction events.</p>
+<p><strong>TrIdent - Transduction Identification</strong> <a href="https://jlmaier12.github.io/TrIdent/"><img src="reference/figures/logo.png" align="right" height="139" alt="TrIdent website"></a></p>
+<p><strong>TrIdent automates the analysis of transductomics data by detecting, classifying, and characterizing read coverage patterns associated with potential transduction events.</strong></p>
 <p>Transductomics, developed by Kleiner et al. (2020), is a DNA sequencing-based method for the detection and characterization of transduction events in pure cultures and complex communities. Transductomics relies on mapping sequencing reads from a viral-like particle (VLP)-fraction of a sample to contigs assembled from the metagenome (whole-community) of the same sample. Reads from bacterial DNA carried by VLPs will map back to the bacterial contigs of origin creating read coverage patterns indicative of ongoing transduction. <strong>The read coverage patterns detected represent DNA being actively carried or transduced by VLPs. The read coverage patterns do not represent complete transduction events (i.e integration of transduced DNA into new bacterial chromosomes).</strong></p>
 <p>To obtain the data needed for transductomics, a microbiome sample of interest is split to prepare two sub-sample types: - Whole-community: Represents the ‘whole-community’ (all bacteria, fungi, virus, etc) in the microbiome of interest - VLP-fraction: Represents only the virus and ‘viral-like particles’ associated with the microbiome of interest - The VLP-fraction must be obtained by an appropriate ultra-purification protocol for your sample type to remove bacterial cells and contaminating free bacterial DNA.</p>
 <p>With transductomics and TrIdent, a researcher can obtain information about the phage-host pairs involved in transduction, the types of transduction occuring, and the region of the host genome that is potentially transduced, which allows exploration of transferred genes.</p>
@@ -88,18 +86,32 @@ <h3 id="input-files">Input files<a class="anchor" aria-label="anchor" href="#inp
 <div class="section level2">
 <h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a>
 </h2>
-<p>You can install the development version of TrIdent from <a href="https://github.com/" class="external-link">GitHub</a> with:</p>
+<p>Install TrIdent with BiocManager:</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="co"># install.packages("pak")</span></span>
-<span><span class="fu">pak</span><span class="fu">::</span><span class="fu">pak</span><span class="op">(</span><span class="st">"jlmaier12/TrIdent"</span><span class="op">)</span></span></code></pre></div>
+<code class="sourceCode R"><span><span class="kw">if</span> <span class="op">(</span><span class="op">!</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://bioconductor.github.io/BiocManager/" class="external-link">"BiocManager"</a></span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span>
+<span>  <span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"BiocManager"</span><span class="op">)</span></span>
+<span><span class="op">}</span></span>
+<span></span>
+<span><span class="fu">BiocManager</span><span class="fu">::</span><span class="fu"><a href="https://bioconductor.github.io/BiocManager/reference/install.html" class="external-link">install</a></span><span class="op">(</span><span class="st">"TrIdent"</span><span class="op">)</span></span>
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/jlmaier12/TrIdent" class="external-link">TrIdent</a></span><span class="op">)</span></span></code></pre></div>
+<p>Install the development version of TrIdent through Github with BiocManager:</p>
+<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="fu">BiocManager</span><span class="fu">::</span><span class="fu"><a href="https://bioconductor.github.io/BiocManager/reference/install.html" class="external-link">install</a></span><span class="op">(</span><span class="st">"jlmaier12/TrIdent"</span><span class="op">)</span></span>
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/jlmaier12/TrIdent" class="external-link">TrIdent</a></span><span class="op">)</span></span></code></pre></div>
 </div>
 <div class="section level2">
 <h2 id="quick-start">Quick Start<a class="anchor" aria-label="anchor" href="#quick-start"></a>
 </h2>
-<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/jlmaier12/TrIdent" class="external-link">TrIdent</a></span><span class="op">)</span></span>
+<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="co">## Load TrIdent</span></span>
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/jlmaier12/TrIdent" class="external-link">TrIdent</a></span><span class="op">)</span></span>
 <span></span>
-<span><span class="co">## Run first</span></span>
+<span><span class="co">## Load sample datasets</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="st">"VLPFractionSamplePileup"</span><span class="op">)</span></span>
+<span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="st">"WholeCommunitySamplePileup"</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co">## Run TrIdent:</span></span>
+<span><span class="co">## Run first:</span></span>
 <span><span class="va">TrIdentOutput</span> <span class="op">&lt;-</span> <span class="fu"><a href="reference/TrIdentClassifier.html">TrIdentClassifier</a></span><span class="op">(</span></span>
 <span>  VLPpileup <span class="op">=</span> <span class="va">VLPFractionSamplePileup</span>,</span>
 <span>  WCpileup <span class="op">=</span> <span class="va">WholeCommunitySamplePileup</span></span>
@@ -111,7 +123,7 @@ <h2 id="quick-start">Quick Start<a class="anchor" aria-label="anchor" href="#qui
 <span><span class="co">#&gt; Almost done with pattern-matching!</span></span>
 <span><span class="co">#&gt; Determining sizes (bp) of pattern matches</span></span>
 <span><span class="co">#&gt; Identifying highly active/abundant or heterogenously integrated</span></span>
-<span><span class="co">#&gt;         Prophage-like elements</span></span>
+<span><span class="co">#&gt;       Prophage-like elements</span></span>
 <span><span class="co">#&gt; Finalizing output</span></span>
 <span><span class="co">#&gt; Execution time: 14.56secs</span></span>
 <span><span class="co">#&gt; 1 contigs were filtered out based on low read coverage</span></span>
@@ -121,25 +133,66 @@ <h2 id="quick-start">Quick Start<a class="anchor" aria-label="anchor" href="#qui
 <span><span class="co">#&gt;                1                1                4                3</span></span>
 <span><span class="co">#&gt; 3 of the prophage-like classifications are highly active or abundant</span></span>
 <span><span class="co">#&gt; 1 of the prophage-like classifications are mixed, i.e. heterogenously</span></span>
-<span><span class="co">#&gt;         integrated into their bacterial host population</span></span></code></pre></div>
-<p><img src="reference/figures/README-example-1.png" width="100%"></p>
-<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span></span>
-<span><span class="co">## Run second</span></span>
-<span><span class="va">TrIdentPlots</span> <span class="op">&lt;-</span> <span class="fu"><a href="reference/plotTrIdentResults.html">plotTrIdentResults</a></span><span class="op">(</span></span>
+<span><span class="co">#&gt;         integrated into their bacterial host population</span></span>
+<span></span>
+<span><span class="co">## Run second:</span></span>
+<span><span class="fu"><a href="reference/plotTrIdentResults.html">plotTrIdentResults</a></span><span class="op">(</span></span>
 <span>  VLPpileup <span class="op">=</span> <span class="va">VLPFractionSamplePileup</span>,</span>
 <span>  WCpileup <span class="op">=</span> <span class="va">WholeCommunitySamplePileup</span>,</span>
 <span>  TrIdentResults <span class="op">=</span> <span class="va">TrIdentOutput</span></span>
 <span><span class="op">)</span></span>
-<span></span>
-<span><span class="co">## Run third</span></span>
-<span><span class="va">SpecTransduc</span> <span class="op">&lt;-</span> <span class="fu"><a href="reference/specializedTransductionID.html">specializedTransductionID</a></span><span class="op">(</span></span>
+<span><span class="co">#&gt; $NODE_62</span></span></code></pre></div>
+<p><img src="reference/figures/README-example-1.png" width="100%"></p>
+<div class="sourceCode" id="cb4"><pre class="sourceCode R"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" tabindex="-1"></a><span class="co">#&gt; </span></span>
+<span id="cb4-2"><a href="#cb4-2" tabindex="-1"></a><span class="co">#&gt; $NODE_135</span></span></code></pre></div>
+<p><img src="reference/figures/README-example-2.png" width="100%"></p>
+<div class="sourceCode" id="cb5"><pre class="sourceCode R"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="co">#&gt; </span></span>
+<span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a><span class="co">#&gt; $NODE_1088</span></span></code></pre></div>
+<p><img src="reference/figures/README-example-3.png" width="100%"></p>
+<div class="sourceCode" id="cb6"><pre class="sourceCode R"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a><span class="co">#&gt; </span></span>
+<span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a><span class="co">#&gt; $NODE_352</span></span></code></pre></div>
+<p><img src="reference/figures/README-example-4.png" width="100%"></p>
+<div class="sourceCode" id="cb7"><pre class="sourceCode R"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1" tabindex="-1"></a><span class="co">#&gt; </span></span>
+<span id="cb7-2"><a href="#cb7-2" tabindex="-1"></a><span class="co">#&gt; $NODE_368</span></span></code></pre></div>
+<p><img src="reference/figures/README-example-5.png" width="100%"></p>
+<div class="sourceCode" id="cb8"><pre class="sourceCode R"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1" tabindex="-1"></a><span class="co">#&gt; </span></span>
+<span id="cb8-2"><a href="#cb8-2" tabindex="-1"></a><span class="co">#&gt; $NODE_560</span></span></code></pre></div>
+<p><img src="reference/figures/README-example-6.png" width="100%"></p>
+<div class="sourceCode" id="cb9"><pre class="sourceCode R"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" tabindex="-1"></a><span class="co">#&gt; </span></span>
+<span id="cb9-2"><a href="#cb9-2" tabindex="-1"></a><span class="co">#&gt; $NODE_617</span></span></code></pre></div>
+<p><img src="reference/figures/README-example-7.png" width="100%"></p>
+<div class="sourceCode" id="cb10"><pre class="sourceCode R"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1" tabindex="-1"></a><span class="co">#&gt; </span></span>
+<span id="cb10-2"><a href="#cb10-2" tabindex="-1"></a><span class="co">#&gt; $NODE_2060</span></span></code></pre></div>
+<p><img src="reference/figures/README-example-8.png" width="100%"></p>
+<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span></span>
+<span><span class="co">## Run third:</span></span>
+<span><span class="fu"><a href="reference/specializedTransductionID.html">specializedTransductionID</a></span><span class="op">(</span></span>
 <span>  VLPpileup <span class="op">=</span> <span class="va">VLPFractionSamplePileup</span>,</span>
 <span>  TrIdentResults <span class="op">=</span> <span class="va">TrIdentOutput</span></span>
 <span><span class="op">)</span></span>
 <span><span class="co">#&gt; 2 contigs have potential specialized transduction</span></span>
 <span><span class="co">#&gt; We recommend that you also view the results of this search with</span></span>
-<span><span class="co">#&gt;       logScale=TRUE</span></span></code></pre></div>
+<span><span class="co">#&gt;       logScale=TRUE</span></span>
+<span><span class="co">#&gt; $summaryTable</span></span>
+<span><span class="co">#&gt;   contigName specTransduc left right lengthLeft lengthRight</span></span>
+<span><span class="co">#&gt; 1    NODE_62          yes  yes    no      45400        &lt;NA&gt;</span></span>
+<span><span class="co">#&gt; 2   NODE_135           no   no    no       &lt;NA&gt;        &lt;NA&gt;</span></span>
+<span><span class="co">#&gt; 3   NODE_368           no   no    no       &lt;NA&gt;        &lt;NA&gt;</span></span>
+<span><span class="co">#&gt; 4   NODE_617          yes  yes   yes      33300        9800</span></span>
+<span><span class="co">#&gt; </span></span>
+<span><span class="co">#&gt; $Plots</span></span>
+<span><span class="co">#&gt; $Plots$NODE_62</span></span></code></pre></div>
+<p><img src="reference/figures/README-example-9.png" width="100%"></p>
+<div class="sourceCode" id="cb12"><pre class="sourceCode R"><code class="sourceCode r"><span id="cb12-1"><a href="#cb12-1" tabindex="-1"></a><span class="co">#&gt; </span></span>
+<span id="cb12-2"><a href="#cb12-2" tabindex="-1"></a><span class="co">#&gt; $Plots$NODE_135</span></span></code></pre></div>
+<p><img src="reference/figures/README-example-10.png" width="100%"></p>
+<div class="sourceCode" id="cb13"><pre class="sourceCode R"><code class="sourceCode r"><span id="cb13-1"><a href="#cb13-1" tabindex="-1"></a><span class="co">#&gt; </span></span>
+<span id="cb13-2"><a href="#cb13-2" tabindex="-1"></a><span class="co">#&gt; $Plots$NODE_368</span></span></code></pre></div>
+<p><img src="reference/figures/README-example-11.png" width="100%"></p>
+<div class="sourceCode" id="cb14"><pre class="sourceCode R"><code class="sourceCode r"><span id="cb14-1"><a href="#cb14-1" tabindex="-1"></a><span class="co">#&gt; </span></span>
+<span id="cb14-2"><a href="#cb14-2" tabindex="-1"></a><span class="co">#&gt; $Plots$NODE_617</span></span></code></pre></div>
+<p><img src="reference/figures/README-example-12.png" width="100%"></p>
 </div>
 </div>
   </main><aside class="col-md-3"><div class="links">
@@ -168,7 +221,7 @@ <h2 data-toc-skip>Citation</h2>
 <div class="developers">
 <h2 data-toc-skip>Developers</h2>
 <ul class="list-unstyled">
-<li>Jessie Maier <br><small class="roles"> Author, maintainer, copyright holder </small> <a href="https://orcid.org/0009-0001-8575-5386" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
+<li>Jessie Maier <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0009-0001-8575-5386" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
 <li>Jorden Rabasco <br><small class="roles"> Author, contributor </small> <a href="https://orcid.org/0000-0002-6971-6678" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
 <li>Craig Gin <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0002-7447-663X" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
 <li>Benjamin Callahan <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0002-8752-117X" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
@@ -176,12 +229,7 @@ <h2 data-toc-skip>Developers</h2>
 </ul>
 </div>
 
-<div class="dev-status">
-<h2 data-toc-skip>Dev status</h2>
-<ul class="list-unstyled">
-<li><a href="https://jlmaier12.github.io/TrIdent/"><img src="reference/figures/logo.png" align="right" height="139" alt="TrIdent website"></a></li>
-</ul>
-</div>
+
 
   </aside>
 </div>
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diff --git a/news/index.html b/news/index.html
index d05e735..bee3b93 100644
--- a/news/index.html
+++ b/news/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,10 +36,30 @@
     </div>
 
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.99.0" id="trident-0990">TrIdent 0.99.0<a class="anchor" aria-label="anchor" href="#trident-0990"></a></h2>
-<ul><li>Initial CRAN submission.</li>
+<h2 class="pkg-version" data-toc-text="0.99.2" id="changes-in-0992">Changes in 0.99.2<a class="anchor" aria-label="anchor" href="#changes-in-0992"></a></h2>
+<ul><li>Updated vignette and README with BiocManager installation instructions</li>
+<li>Moved Acknowledgements, Funding, and SessionInfo() to ‘supplemental information’ section in vignette</li>
+<li>Changed TOC_depth from 2 to 3 in vignette</li>
+<li>Updated formatting of NEWS file</li>
+<li>Grouped related functions in .R files for easier troubleshooting</li>
+<li>Add verbose = TRUE/FALSE argument to allow users to choose whether to print progress</li>
+<li>Added co-authors to DESCRIPTION file</li>
+<li>Added additional logic for input file validation</li>
+<li>Added better descriptions of input file requirements in the main function .man pages</li>
+<li>Added rendered summary histogram plot to output list</li>
+<li>Removed all usage of &lt;&lt;-</li>
+<li>Fixed improper usage of lapply</li>
 </ul></div>
-  </main></div>
+    <div class="section level2">
+<h2 class="pkg-version" data-toc-text="0.99.1" id="changes-in-0991">Changes in 0.99.1<a class="anchor" aria-label="anchor" href="#changes-in-0991"></a></h2>
+<ul><li>Fixed unit tests for Bioc submission</li>
+</ul></div>
+    <div class="section level2">
+<h2 class="pkg-version" data-toc-text="0.99.0" id="changes-in-0990">Changes in 0.99.0<a class="anchor" aria-label="anchor" href="#changes-in-0990"></a></h2>
+<ul><li>Bioc submission</li>
+</ul></div>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
diff --git a/pkgdown.yml b/pkgdown.yml
index 3a5f913..304510f 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.1.1
 pkgdown_sha: ~
 articles:
   TrIdent-vignette: TrIdent-vignette.html
-last_built: 2024-12-20T17:05Z
+last_built: 2025-01-02T20:52Z
 urls:
   reference: https://jlmaier12.github.io/TrIdent/reference
   article: https://jlmaier12.github.io/TrIdent/articles
diff --git a/reference/NARemover.html b/reference/NARemover.html
index 40c7130..be62584 100644
--- a/reference/NARemover.html
+++ b/reference/NARemover.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -32,7 +32,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>NA remover</h1>
-      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/Utils.R" class="external-link"><code>R/Utils.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/UtilFunctions.R" class="external-link"><code>R/UtilFunctions.R</code></a></small>
       <div class="d-none name"><code>NARemover.Rd</code></div>
     </div>
 
diff --git a/reference/TrIdent-package.html b/reference/TrIdent-package.html
index a77eeb3..98e81aa 100644
--- a/reference/TrIdent-package.html
+++ b/reference/TrIdent-package.html
@@ -19,7 +19,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/TrIdentClassifier.html b/reference/TrIdentClassifier.html
index ec3807d..fd4e253 100644
--- a/reference/TrIdentClassifier.html
+++ b/reference/TrIdentClassifier.html
@@ -23,7 +23,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -75,6 +75,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 <span>  minContigLength <span class="op">=</span> <span class="fl">30000</span>,</span>
 <span>  minSlope <span class="op">=</span> <span class="fl">0.001</span>,</span>
 <span>  suggFiltThresh <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  verbose <span class="op">=</span> <span class="cn">TRUE</span>,</span>
 <span>  <span class="va">SaveFilesTo</span></span>
 <span><span class="op">)</span></span></code></pre></div>
     </div>
@@ -84,11 +85,27 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dl><dt id="arg-vlppileup">VLPpileup<a class="anchor" aria-label="anchor" href="#arg-vlppileup"></a></dt>
-<dd><p>VLP-fraction pileup file.</p></dd>
+<dd><p>VLP-fraction pileup file generated by mapping sequencing reads
+from a sample's ultra-purified VLP-fraction mapped to the sample's whole-community
+metagenome assembly. The pileup file MUST have the following format:
+* V1: Contig accession
+* V2: Mapped read coverage values averaged over 100 bp windows
+* V3: Starting position (bp) of each 100 bp window. Restarts from 0 at the
+start of each new contig.
+* V4: Starting position (bp) of each 100 bp window. Does NOT restart at the
+start of each new contig.</p></dd>
 
 
 <dt id="arg-wcpileup">WCpileup<a class="anchor" aria-label="anchor" href="#arg-wcpileup"></a></dt>
-<dd><p>A whole-community pileup file.</p></dd>
+<dd><p>A whole-community pileup file generated by mapping sequencing reads
+from a sample's whole-community mapped to the sample's whole-community metagenome assembly.
+The pileup file MUST have the following format:
+* V1: Contig accession
+* V2: Mapped read coverage values averaged over 100 bp windows
+* V3: Starting position (bp) of each 100 bp window. Restarts from 0 at the
+start of each new contig.
+* V4: Starting position (bp) of each 100 bp window. Does NOT restart at the
+start of each new contig.</p></dd>
 
 
 <dt id="arg-windowsize">windowSize<a class="anchor" aria-label="anchor" href="#arg-windowsize"></a></dt>
@@ -122,6 +139,10 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 Default is FALSE.</p></dd>
 
 
+<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
+<dd><p>TRUE or FALSE. Print progress messages to console. Default is TRUE.</p></dd>
+
+
 <dt id="arg-savefilesto">SaveFilesTo<a class="anchor" aria-label="anchor" href="#arg-savefilesto"></a></dt>
 <dd><p>Optional, Provide a path to the directory you wish to save
 output to. A folder will be made within the provided directory to store
@@ -135,7 +156,10 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">TrIdent_results</span> <span class="op">&lt;-</span> <span class="fu">TrIdentClassifier</span><span class="op">(</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="st">"VLPFractionSamplePileup"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="st">"WholeCommunitySamplePileup"</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="va">TrIdent_results</span> <span class="op">&lt;-</span> <span class="fu">TrIdentClassifier</span><span class="op">(</span></span></span>
 <span class="r-in"><span>  VLPpileup <span class="op">=</span> <span class="va">VLPFractionSamplePileup</span>,</span></span>
 <span class="r-in"><span>  WCpileup <span class="op">=</span> <span class="va">WholeCommunitySamplePileup</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
@@ -146,9 +170,9 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Almost done with pattern-matching!</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Determining sizes (bp) of pattern matches</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Identifying highly active/abundant or heterogenously integrated</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>         Prophage-like elements</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>       Prophage-like elements</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Finalizing output</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Execution time: 14.75secs</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Execution time: 27.2secs</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> 1 contigs were filtered out based on low read coverage</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> 0 contigs were filtered out based on length</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
@@ -157,7 +181,6 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-msg co"><span class="r-pr">#&gt;</span> 3 of the prophage-like classifications are highly active or abundant</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> 1 of the prophage-like classifications are mixed, i.e. heterogenously</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>         integrated into their bacterial host population</span>
-<span class="r-plt img"><img src="TrIdentClassifier-1.png" alt="" width="700" height="433"></span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
diff --git a/reference/TrIdentSampleOutput.html b/reference/TrIdentSampleOutput.html
index c69f6b9..2ec0447 100644
--- a/reference/TrIdentSampleOutput.html
+++ b/reference/TrIdentSampleOutput.html
@@ -1,7 +1,9 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>TrIdentSampleOutput — TrIdentSampleOutput • TrIdent</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="TrIdentSampleOutput — TrIdentSampleOutput"><meta name="description" content="The TrIdentClassifier output from the VLPFractionSamplePileup and
-WholeCommunitySamplePileup files run with default parameters Report..."><meta property="og:description" content="The TrIdentClassifier output from the VLPFractionSamplePileup and
-WholeCommunitySamplePileup files run with default parameters Report..."><meta property="og:image" content="https://jlmaier12.github.io/TrIdent/logo.png"></head><body>
+WholeCommunitySamplePileup files run with default parameters
+Report..."><meta property="og:description" content="The TrIdentClassifier output from the VLPFractionSamplePileup and
+WholeCommunitySamplePileup files run with default parameters
+Report..."><meta property="og:image" content="https://jlmaier12.github.io/TrIdent/logo.png"></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
 
@@ -9,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -40,7 +42,8 @@
 
     <div class="ref-description section level2">
     <p>The TrIdentClassifier output from the VLPFractionSamplePileup and
-WholeCommunitySamplePileup files run with default parameters Report...</p>
+WholeCommunitySamplePileup files run with default parameters
+Report...</p>
     </div>
 
     <div class="section level2">
@@ -50,7 +53,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
     <div class="section level2">
     <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
-    <p>## 'TrIdentSampleOutput' A list with 5 objects:</p><dl><dt>SummaryTable</dt>
+    <p>## 'TrIdentSampleOutput' A list with 6 objects:</p><dl><dt>SummaryTable</dt>
 <dd><p>A dataframe containing classifications for all
    contigs that were processed with pattern-matching</p></dd>
 
@@ -69,6 +72,14 @@ <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a><
    <dt>windowSize</dt>
 <dd><p>windowSize used in TrIdentClassifier function (1000)</p></dd>
 
+   <dt>ResultHistogram</dt>
+<dd><p>a histogram displaying the overall abundance and
+   quality of pattern-matches in addition to the composition of
+   classifications. The displayed pattern-match scores are normalized by
+   dividing each score by its associated contig length. The scores are
+   normalized to visualize the overall quality of pattern-matching for the
+   entire dataset.</p></dd>
+
 
 </dl></div>
     <div class="section level2">
diff --git a/reference/VLPFractionSamplePileup.html b/reference/VLPFractionSamplePileup.html
index 3287f36..0c85193 100644
--- a/reference/VLPFractionSamplePileup.html
+++ b/reference/VLPFractionSamplePileup.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -88,7 +88,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 NODE_617:Prophage-like, active/abundant, with spec transduction
 NODE_135:Prophage-like, off one side of contig, no spec transduction
 NODE_352:Sloping, left to right slope
-NODE_251: Sloping, right to left slope
+NODE_1088: Sloping, right to left slope
 NODE_2060: Sloping, right to left slope with start
 NODE_1401: None, no pattern match
 NODE_62: Prophage-like, with spec transduction
diff --git a/reference/VLPtoWCRatioCalc.html b/reference/VLPtoWCRatioCalc.html
index a2cc559..1e68303 100644
--- a/reference/VLPtoWCRatioCalc.html
+++ b/reference/VLPtoWCRatioCalc.html
@@ -15,7 +15,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -40,7 +40,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>VLP-fraction:whole-community read coverage ratio calculator</h1>
-      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/patternCharacterization.R" class="external-link"><code>R/patternCharacterization.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/patternCharacterizationFunctions.R" class="external-link"><code>R/patternCharacterizationFunctions.R</code></a></small>
       <div class="d-none name"><code>VLPtoWCRatioCalc.Rd</code></div>
     </div>
 
diff --git a/reference/WholeCommunitySamplePileup.html b/reference/WholeCommunitySamplePileup.html
index 16360c6..afc9430 100644
--- a/reference/WholeCommunitySamplePileup.html
+++ b/reference/WholeCommunitySamplePileup.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -88,7 +88,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 NODE_617:Prophage-like, active/abundant, with spec transduction
 NODE_135:Prophage-like, off one side of contig, no spec transduction
 NODE_352:Sloping, left to right slope
-NODE_251: Sloping, right to left slope
+NODE_1088: Sloping, right to left slope
 NODE_2060: Sloping, right to left slope with start
 NODE_1401: None, no pattern match
 NODE_62: Prophage-like, with spec transduction
diff --git a/reference/allPatternMatches.html b/reference/allPatternMatches.html
index d65c5dd..6ea1156 100644
--- a/reference/allPatternMatches.html
+++ b/reference/allPatternMatches.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -34,7 +34,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Collects pattern-match information for all classifications</h1>
-      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/resultsSummary.R" class="external-link"><code>R/resultsSummary.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/summarizeResultsFunctions.R" class="external-link"><code>R/summarizeResultsFunctions.R</code></a></small>
       <div class="d-none name"><code>allPatternMatches.Rd</code></div>
     </div>
 
diff --git a/reference/allProphageLikeClassifs.html b/reference/allProphageLikeClassifs.html
index b5ff5cd..f662fc8 100644
--- a/reference/allProphageLikeClassifs.html
+++ b/reference/allProphageLikeClassifs.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -34,7 +34,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Collects Prophage-like classification pattern-match information</h1>
-      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/resultsSummary.R" class="external-link"><code>R/resultsSummary.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/summarizeResultsFunctions.R" class="external-link"><code>R/summarizeResultsFunctions.R</code></a></small>
       <div class="d-none name"><code>allProphageLikeClassifs.Rd</code></div>
     </div>
 
diff --git a/reference/allSlopingClassifs.html b/reference/allSlopingClassifs.html
index 852ba14..e601937 100644
--- a/reference/allSlopingClassifs.html
+++ b/reference/allSlopingClassifs.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -34,7 +34,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Collects Sloping classification pattern-match i nformation</h1>
-      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/resultsSummary.R" class="external-link"><code>R/resultsSummary.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/summarizeResultsFunctions.R" class="external-link"><code>R/summarizeResultsFunctions.R</code></a></small>
       <div class="d-none name"><code>allSlopingClassifs.Rd</code></div>
     </div>
 
diff --git a/reference/blockBuilder.html b/reference/blockBuilder.html
index 1ff9564..3230d99 100644
--- a/reference/blockBuilder.html
+++ b/reference/blockBuilder.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -34,7 +34,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Builds prophage-like block patterns</h1>
-      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/blockPatterns.R" class="external-link"><code>R/blockPatterns.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/blockPatternFunctions.R" class="external-link"><code>R/blockPatternFunctions.R</code></a></small>
       <div class="d-none name"><code>blockBuilder.Rd</code></div>
     </div>
 
diff --git a/reference/blockTranslator.html b/reference/blockTranslator.html
index 5778433..7cf55ea 100644
--- a/reference/blockTranslator.html
+++ b/reference/blockTranslator.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,7 +36,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Full block pattern-translator</h1>
-      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/blockPatterns.R" class="external-link"><code>R/blockPatterns.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/blockPatternFunctions.R" class="external-link"><code>R/blockPatternFunctions.R</code></a></small>
       <div class="d-none name"><code>blockTranslator.Rd</code></div>
     </div>
 
diff --git a/reference/changeSlope.html b/reference/changeSlope.html
index 5b05d92..d469047 100644
--- a/reference/changeSlope.html
+++ b/reference/changeSlope.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -32,7 +32,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Change slope of sloping pattern</h1>
-      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/fullSlopingPatterns.R" class="external-link"><code>R/fullSlopingPatterns.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/fullSlopingPatternFunctions.R" class="external-link"><code>R/fullSlopingPatternFunctions.R</code></a></small>
       <div class="d-none name"><code>changeSlope.Rd</code></div>
     </div>
 
diff --git a/reference/changeSlopeWStart.html b/reference/changeSlopeWStart.html
index 43243e4..0e5325a 100644
--- a/reference/changeSlopeWStart.html
+++ b/reference/changeSlopeWStart.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -32,7 +32,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Change slope of sloping pattern with initial start</h1>
-      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/partialSlopingPatterns.R" class="external-link"><code>R/partialSlopingPatterns.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/partialSlopingPatternFunctions.R" class="external-link"><code>R/partialSlopingPatternFunctions.R</code></a></small>
       <div class="d-none name"><code>changeSlopeWStart.Rd</code></div>
     </div>
 
diff --git a/reference/changeWindowSize.html b/reference/changeWindowSize.html
index 69410c7..8d656ea 100644
--- a/reference/changeWindowSize.html
+++ b/reference/changeWindowSize.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -34,7 +34,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Change the read coverage rolling mean window size</h1>
-      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/Utils.R" class="external-link"><code>R/Utils.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/UtilFunctions.R" class="external-link"><code>R/UtilFunctions.R</code></a></small>
       <div class="d-none name"><code>changeWindowSize.Rd</code></div>
     </div>
 
diff --git a/reference/contigClassSumm.html b/reference/contigClassSumm.html
index d661791..ea939e0 100644
--- a/reference/contigClassSumm.html
+++ b/reference/contigClassSumm.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -34,7 +34,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Summarizes pattern-match information</h1>
-      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/patternCharacterization.R" class="external-link"><code>R/patternCharacterization.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/patternCharacterizationFunctions.R" class="external-link"><code>R/patternCharacterizationFunctions.R</code></a></small>
       <div class="d-none name"><code>contigClassSumm.Rd</code></div>
     </div>
 
diff --git a/reference/figures/README-example-1.png b/reference/figures/README-example-1.png
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Jg-Van{|jAriMap(

literal 0
HcmV?d00001

diff --git a/reference/figures/README-example-12.png b/reference/figures/README-example-12.png
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diff --git a/reference/fullSlope.html b/reference/fullSlope.html
index 3a4787e..2f90fad 100644
--- a/reference/fullSlope.html
+++ b/reference/fullSlope.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,7 +36,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Sloping pattern builder</h1>
-      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/fullSlopingPatterns.R" class="external-link"><code>R/fullSlopingPatterns.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/fullSlopingPatternFunctions.R" class="external-link"><code>R/fullSlopingPatternFunctions.R</code></a></small>
       <div class="d-none name"><code>fullSlope.Rd</code></div>
     </div>
 
diff --git a/reference/index.html b/reference/index.html
index 8a61206..1cdedb8 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/leftRightBlockTranslater.html b/reference/leftRightBlockTranslater.html
index a0f88c1..7473fd1 100644
--- a/reference/leftRightBlockTranslater.html
+++ b/reference/leftRightBlockTranslater.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -32,7 +32,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Translate left and right block patterns across contig</h1>
-      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/blockPatterns.R" class="external-link"><code>R/blockPatterns.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/blockPatternFunctions.R" class="external-link"><code>R/blockPatternFunctions.R</code></a></small>
       <div class="d-none name"><code>leftRightBlockTranslater.Rd</code></div>
     </div>
 
diff --git a/reference/makeBlockPattern.html b/reference/makeBlockPattern.html
index c44c418..a682066 100644
--- a/reference/makeBlockPattern.html
+++ b/reference/makeBlockPattern.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -32,7 +32,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Make block patterns for pattern-matching</h1>
-      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/blockPatterns.R" class="external-link"><code>R/blockPatterns.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/blockPatternFunctions.R" class="external-link"><code>R/blockPatternFunctions.R</code></a></small>
       <div class="d-none name"><code>makeBlockPattern.Rd</code></div>
     </div>
 
diff --git a/reference/makeFullSlopes.html b/reference/makeFullSlopes.html
index e39c3cd..216eb5c 100644
--- a/reference/makeFullSlopes.html
+++ b/reference/makeFullSlopes.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -34,7 +34,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Make full slope patterns</h1>
-      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/fullSlopingPatterns.R" class="external-link"><code>R/fullSlopingPatterns.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/fullSlopingPatternFunctions.R" class="external-link"><code>R/fullSlopingPatternFunctions.R</code></a></small>
       <div class="d-none name"><code>makeFullSlopes.Rd</code></div>
     </div>
 
diff --git a/reference/makeSlopesWStarts.html b/reference/makeSlopesWStarts.html
index 72f5fe7..33e5757 100644
--- a/reference/makeSlopesWStarts.html
+++ b/reference/makeSlopesWStarts.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,7 +36,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Make slope patterns with starts</h1>
-      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/partialSlopingPatterns.R" class="external-link"><code>R/partialSlopingPatterns.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/partialSlopingPatternFunctions.R" class="external-link"><code>R/partialSlopingPatternFunctions.R</code></a></small>
       <div class="d-none name"><code>makeSlopesWStarts.Rd</code></div>
     </div>
 
diff --git a/reference/noPattern.html b/reference/noPattern.html
index c958d10..9d05be8 100644
--- a/reference/noPattern.html
+++ b/reference/noPattern.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/patternBuilder.html b/reference/patternBuilder.html
index 536a66c..f330df4 100644
--- a/reference/patternBuilder.html
+++ b/reference/patternBuilder.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -34,7 +34,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Pattern-builder</h1>
-      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/plottingTrIdentResults.R" class="external-link"><code>R/plottingTrIdentResults.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/plottingTrIdentResultsFunctions.R" class="external-link"><code>R/plottingTrIdentResultsFunctions.R</code></a></small>
       <div class="d-none name"><code>patternBuilder.Rd</code></div>
     </div>
 
diff --git a/reference/patternMatchSize.html b/reference/patternMatchSize.html
index d6c6d8b..3631ab5 100644
--- a/reference/patternMatchSize.html
+++ b/reference/patternMatchSize.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -34,7 +34,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Pattern-match size calculator</h1>
-      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/patternCharacterization.R" class="external-link"><code>R/patternCharacterization.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/patternCharacterizationFunctions.R" class="external-link"><code>R/patternCharacterizationFunctions.R</code></a></small>
       <div class="d-none name"><code>patternMatchSize.Rd</code></div>
     </div>
 
@@ -45,7 +45,7 @@
 
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">patternMatchSize</span><span class="op">(</span><span class="va">classifSumm</span>, <span class="va">classifList</span>, <span class="va">windowSize</span><span class="op">)</span></span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">patternMatchSize</span><span class="op">(</span><span class="va">classifSumm</span>, <span class="va">classifList</span>, <span class="va">windowSize</span>, <span class="va">verbose</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
@@ -64,6 +64,11 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 <dt id="arg-windowsize">windowSize<a class="anchor" aria-label="anchor" href="#arg-windowsize"></a></dt>
 <dd><p>The window size used to re-average read coverage pileups</p></dd>
 
+
+<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
+<dd><p>TRUE or FALSE. Print progress messages to console. Default is
+TRUE.</p></dd>
+
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
diff --git a/reference/patternMatcher.html b/reference/patternMatcher.html
index 6efb68c..1f8b00e 100644
--- a/reference/patternMatcher.html
+++ b/reference/patternMatcher.html
@@ -17,7 +17,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/pileupFormatter.html b/reference/pileupFormatter.html
index 66d2547..eb81544 100644
--- a/reference/pileupFormatter.html
+++ b/reference/pileupFormatter.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -34,7 +34,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Correctly formats pileup files.</h1>
-      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/Utils.R" class="external-link"><code>R/Utils.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/UtilFunctions.R" class="external-link"><code>R/UtilFunctions.R</code></a></small>
       <div class="d-none name"><code>pileupFormatter.Rd</code></div>
     </div>
 
diff --git a/reference/plotTrIdentResults.html b/reference/plotTrIdentResults.html
index 1566f6e..8101004 100644
--- a/reference/plotTrIdentResults.html
+++ b/reference/plotTrIdentResults.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,7 +36,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Plot read coverage graphs of contigs classified as Prophage-like, Sloping, or HighCovNoPattern</h1>
-      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/plottingTrIdentResults.R" class="external-link"><code>R/plottingTrIdentResults.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/plottingTrIdentResultsFunctions.R" class="external-link"><code>R/plottingTrIdentResultsFunctions.R</code></a></small>
       <div class="d-none name"><code>plotTrIdentResults.Rd</code></div>
     </div>
 
@@ -62,11 +62,27 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dl><dt id="arg-vlppileup">VLPpileup<a class="anchor" aria-label="anchor" href="#arg-vlppileup"></a></dt>
-<dd><p>VLP-fraction pileup file.</p></dd>
+<dd><p>VLP-fraction pileup file generated by mapping sequencing reads
+from a sample's ultra-purified VLP-fraction mapped to the sample's whole-community
+metagenome assembly. The pileup file MUST have the following format:
+* V1: Contig accession
+* V2: Mapped read coverage values averaged over 100 bp windows
+* V3: Starting position (bp) of each 100 bp window. Restarts from 0 at the
+start of each new contig.
+* V4: Starting position (bp) of each 100 bp window. Does NOT restart at the
+start of each new contig.</p></dd>
 
 
 <dt id="arg-wcpileup">WCpileup<a class="anchor" aria-label="anchor" href="#arg-wcpileup"></a></dt>
-<dd><p>Whole-community pileup file.</p></dd>
+<dd><p>A whole-community pileup file generated by mapping sequencing reads
+from a sample's whole-community mapped to the sample's whole-community metagenome assembly.
+The pileup file MUST have the following format:
+* V1: Contig accession
+* V2: Mapped read coverage values averaged over 100 bp windows
+* V3: Starting position (bp) of each 100 bp window. Restarts from 0 at the
+start of each new contig.
+* V4: Starting position (bp) of each 100 bp window. Does NOT restart at the
+start of each new contig.</p></dd>
 
 
 <dt id="arg-tridentresults">TrIdentResults<a class="anchor" aria-label="anchor" href="#arg-tridentresults"></a></dt>
@@ -92,7 +108,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">patternMatches</span> <span class="op">&lt;-</span> <span class="fu">plotTrIdentResults</span><span class="op">(</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="st">"VLPFractionSamplePileup"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="st">"WholeCommunitySamplePileup"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="st">"TrIdentSampleOutput"</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="va">patternMatches</span> <span class="op">&lt;-</span> <span class="fu">plotTrIdentResults</span><span class="op">(</span></span></span>
 <span class="r-in"><span>  VLPpileup <span class="op">=</span> <span class="va">VLPFractionSamplePileup</span>,</span></span>
 <span class="r-in"><span>  WCpileup <span class="op">=</span> <span class="va">WholeCommunitySamplePileup</span>,</span></span>
 <span class="r-in"><span>  TrIdentResults <span class="op">=</span> <span class="va">TrIdentSampleOutput</span></span></span>
diff --git a/reference/prophageLikeBorders.html b/reference/prophageLikeBorders.html
index bfb2ada..764551d 100644
--- a/reference/prophageLikeBorders.html
+++ b/reference/prophageLikeBorders.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,7 +36,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Prophage-like border finder</h1>
-      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/specializedTransductionHelpers.R" class="external-link"><code>R/specializedTransductionHelpers.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/specializedTransductionHelperFunctions.R" class="external-link"><code>R/specializedTransductionHelperFunctions.R</code></a></small>
       <div class="d-none name"><code>prophageLikeBorders.Rd</code></div>
     </div>
 
diff --git a/reference/prophageLikeElevation.html b/reference/prophageLikeElevation.html
index dd5bff9..4a8c578 100644
--- a/reference/prophageLikeElevation.html
+++ b/reference/prophageLikeElevation.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,7 +36,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Determine Prophage-like read coverage elevation in whole-community</h1>
-      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/patternCharacterization.R" class="external-link"><code>R/patternCharacterization.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/patternCharacterizationFunctions.R" class="external-link"><code>R/patternCharacterizationFunctions.R</code></a></small>
       <div class="d-none name"><code>prophageLikeElevation.Rd</code></div>
     </div>
 
@@ -53,7 +53,8 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 <span>  <span class="va">prophageLikeClassifList</span>,</span>
 <span>  <span class="va">VLPpileup</span>,</span>
 <span>  <span class="va">WCpileup</span>,</span>
-<span>  <span class="va">windowSize</span></span>
+<span>  <span class="va">windowSize</span>,</span>
+<span>  <span class="va">verbose</span></span>
 <span><span class="op">)</span></span></code></pre></div>
     </div>
 
@@ -85,6 +86,11 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 <dt id="arg-windowsize">windowSize<a class="anchor" aria-label="anchor" href="#arg-windowsize"></a></dt>
 <dd><p>The window size used to re-average read coverage pileups</p></dd>
 
+
+<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
+<dd><p>TRUE or FALSE. Print progress messages to console. Default is
+TRUE.</p></dd>
+
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
diff --git a/reference/prophageLikeZoom.html b/reference/prophageLikeZoom.html
index e2868de..c4285cd 100644
--- a/reference/prophageLikeZoom.html
+++ b/reference/prophageLikeZoom.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -32,7 +32,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Prophage-like pattern zoom</h1>
-      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/specializedTransductionHelpers.R" class="external-link"><code>R/specializedTransductionHelpers.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/specializedTransductionHelperFunctions.R" class="external-link"><code>R/specializedTransductionHelperFunctions.R</code></a></small>
       <div class="d-none name"><code>prophageLikeZoom.Rd</code></div>
     </div>
 
diff --git a/reference/resultsHisto.html b/reference/resultsHisto.html
index 771bae3..823a5d2 100644
--- a/reference/resultsHisto.html
+++ b/reference/resultsHisto.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/slopeSumm.html b/reference/slopeSumm.html
index 6fd27d0..30d1f3f 100644
--- a/reference/slopeSumm.html
+++ b/reference/slopeSumm.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -32,7 +32,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Summarize slopes for sloping classifications</h1>
-      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/patternCharacterization.R" class="external-link"><code>R/patternCharacterization.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/patternCharacterizationFunctions.R" class="external-link"><code>R/patternCharacterizationFunctions.R</code></a></small>
       <div class="d-none name"><code>slopeSumm.Rd</code></div>
     </div>
 
diff --git a/reference/slopeTranslator.html b/reference/slopeTranslator.html
index 171b6d1..cdf10ee 100644
--- a/reference/slopeTranslator.html
+++ b/reference/slopeTranslator.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,7 +36,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Sloping pattern translator</h1>
-      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/partialSlopingPatterns.R" class="external-link"><code>R/partialSlopingPatterns.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/partialSlopingPatternFunctions.R" class="external-link"><code>R/partialSlopingPatternFunctions.R</code></a></small>
       <div class="d-none name"><code>slopeTranslator.Rd</code></div>
     </div>
 
diff --git a/reference/slopeWithStart.html b/reference/slopeWithStart.html
index f6b83ba..f125dc9 100644
--- a/reference/slopeWithStart.html
+++ b/reference/slopeWithStart.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -32,7 +32,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Sloping pattern with an initial jump-up in read coverage</h1>
-      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/partialSlopingPatterns.R" class="external-link"><code>R/partialSlopingPatterns.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/partialSlopingPatternFunctions.R" class="external-link"><code>R/partialSlopingPatternFunctions.R</code></a></small>
       <div class="d-none name"><code>slopeWithStart.Rd</code></div>
     </div>
 
diff --git a/reference/specTransductionPlot.html b/reference/specTransductionPlot.html
index 1c3a34f..7a6d37c 100644
--- a/reference/specTransductionPlot.html
+++ b/reference/specTransductionPlot.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -32,7 +32,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Specialized transduction plot</h1>
-      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/specializedTransductionHelpers.R" class="external-link"><code>R/specializedTransductionHelpers.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/specializedTransductionHelperFunctions.R" class="external-link"><code>R/specializedTransductionHelperFunctions.R</code></a></small>
       <div class="d-none name"><code>specTransductionPlot.Rd</code></div>
     </div>
 
diff --git a/reference/specTransductionSearch.html b/reference/specTransductionSearch.html
index 8cd49d9..e26e8e9 100644
--- a/reference/specTransductionSearch.html
+++ b/reference/specTransductionSearch.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -34,7 +34,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Specialized transduction search and plot</h1>
-      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/specializedTransductionHelpers.R" class="external-link"><code>R/specializedTransductionHelpers.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/specializedTransductionHelperFunctions.R" class="external-link"><code>R/specializedTransductionHelperFunctions.R</code></a></small>
       <div class="d-none name"><code>specTransductionSearch.Rd</code></div>
     </div>
 
diff --git a/reference/specializedTransductionID.html b/reference/specializedTransductionID.html
index fdd1d6c..4465070 100644
--- a/reference/specializedTransductionID.html
+++ b/reference/specializedTransductionID.html
@@ -17,7 +17,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -65,6 +65,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 <span>  specTransLength <span class="op">=</span> <span class="fl">2000</span>,</span>
 <span>  <span class="va">matchScoreFilter</span>,</span>
 <span>  logScale <span class="op">=</span> <span class="cn">FALSE</span>,</span>
+<span>  verbose <span class="op">=</span> <span class="cn">TRUE</span>,</span>
 <span>  <span class="va">SaveFilesTo</span></span>
 <span><span class="op">)</span></span></code></pre></div>
     </div>
@@ -74,7 +75,15 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dl><dt id="arg-vlppileup">VLPpileup<a class="anchor" aria-label="anchor" href="#arg-vlppileup"></a></dt>
-<dd><p>VLP-fraction pileup file.</p></dd>
+<dd><p>VLP-fraction pileup file generated by mapping sequencing reads
+from a sample's ultra-purified VLP-fraction mapped to the sample's whole-community
+metagenome assembly. The pileup file MUST have the following format:
+* V1: Contig accession
+* V2: Mapped read coverage values averaged over 100 bp windows
+* V3: Starting position (bp) of each 100 bp window. Restarts from 0 at the
+start of each new contig.
+* V4: Starting position (bp) of each 100 bp window. Does NOT restart at the
+start of each new contig.</p></dd>
 
 
 <dt id="arg-tridentresults">TrIdentResults<a class="anchor" aria-label="anchor" href="#arg-tridentresults"></a></dt>
@@ -109,6 +118,10 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 scale. Default is FALSE.</p></dd>
 
 
+<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
+<dd><p>TRUE or FALSE. Print progress messages to console. Default is TRUE.</p></dd>
+
+
 <dt id="arg-savefilesto">SaveFilesTo<a class="anchor" aria-label="anchor" href="#arg-savefilesto"></a></dt>
 <dd><p>Provide a path to the directory you wish to save output
 to. `specializedTransductionID()` will make a folder within the provided
@@ -122,7 +135,10 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">specTransduction</span> <span class="op">&lt;-</span> <span class="fu">specializedTransductionID</span><span class="op">(</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="st">"VLPFractionSamplePileup"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="st">"TrIdentSampleOutput"</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="va">specTransduction</span> <span class="op">&lt;-</span> <span class="fu">specializedTransductionID</span><span class="op">(</span></span></span>
 <span class="r-in"><span>  VLPpileup <span class="op">=</span> <span class="va">VLPFractionSamplePileup</span>,</span></span>
 <span class="r-in"><span>  TrIdentResults <span class="op">=</span> <span class="va">TrIdentSampleOutput</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
diff --git a/reference/zeroCountSearch.html b/reference/zeroCountSearch.html
index 41fb7fc..1e3d9fa 100644
--- a/reference/zeroCountSearch.html
+++ b/reference/zeroCountSearch.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">TrIdent</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.0.9000</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.99.2</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -36,7 +36,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.png" class="logo" alt=""><h1>Counts zero values to the left and right of prophage-like borders</h1>
-      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/specializedTransductionHelpers.R" class="external-link"><code>R/specializedTransductionHelpers.R</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/jlmaier12/TrIdent/blob/HEAD/R/specializedTransductionHelperFunctions.R" class="external-link"><code>R/specializedTransductionHelperFunctions.R</code></a></small>
       <div class="d-none name"><code>zeroCountSearch.Rd</code></div>
     </div>
 
diff --git a/search.json b/search.json
index 50e507d..774a375 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"TrIdent","text":"TrIdent- Transduction Identification TrIdent consists three main functions run following order: TrIdentClassifier(): Classifies contigs ‘Prophage-like’, ‘Sloping’, ‘HighCovNoPattern’, ‘NoPattern’ using read coverage pattern-matching. plotTrIdentResults(): Plots pattern-matching results TrIdentClassifier(). specializedTransductionID(): Searches contigs classified Prophage-like TrIdentClassifier() associated specialized transduction events. TrIdent automates analysis transductomics data detecting, classifying, characterizing read coverage patterns associated potential transduction events. Transductomics, developed Kleiner et al.  (2020), DNA sequencing-based method detection characterization transduction events pure cultures complex communities. Transductomics relies mapping sequencing reads viral-like particle (VLP)-fraction sample contigs assembled metagenome (whole-community) sample. Reads bacterial DNA carried VLPs map back bacterial contigs origin creating read coverage patterns indicative ongoing transduction. read coverage patterns detected represent DNA actively carried transduced VLPs. read coverage patterns represent complete transduction events (.e integration transduced DNA new bacterial chromosomes). Reference: Kleiner, M., Bushnell, B., Sanderson, K.E. et al.  Transductomics: sequencing-based detection analysis transduced DNA pure cultures microbial communities. Microbiome 8, 158 (2020). https://doi.org/10.1186/s40168-020-00935-5","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"acknowledgments","dir":"Articles","previous_headings":"Introduction","what":"Acknowledgments","title":"TrIdent","text":"TrIdent result combined effort brain power many individuals. Specifically, like thank Dr. Manuel Kleiner, Dr. Ben Callahan, Dr. Breck Duerkop Dr. Craig Gin individual expertise overall support!","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"funding","dir":"Articles","previous_headings":"Introduction","what":"Funding","title":"TrIdent","text":"development TrIdent supported seed grant North Carolina State University Data Science Academy National Institutes Health Award Numbers R35GM138362 R01Al171046.","code":""},{"path":[]},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"cran-install","dir":"Articles","previous_headings":"Installation","what":"CRAN install","title":"TrIdent","text":"","code":"if (!require(\"pak\", quietly = TRUE)) {   install.packages(\"pak\") }  pak::pak(\"jlmaier12/TrIdent\") library(TrIdent)"},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"github-install","dir":"Articles","previous_headings":"Installation","what":"GitHub install","title":"TrIdent","text":"","code":"if (!require(\"devtools\", quietly = TRUE)) {   install.packages(\"devtools\") }  devtools::install_github(\"jlmaier12/TrIdent\") library(TrIdent)"},{"path":[]},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"transductomics-data","dir":"Articles","previous_headings":"Input Data","what":"Transductomics data","title":"TrIdent","text":"Transductomics allows identification bacterial DNA actively carried transduced VLPs. transductomics dataset consists two parts- metagenomes whole-community VLP fractions sample. whole-community fraction generated extracting sequencing DNA whole sample. VLP-fraction generated extraction sequencing DNA ultra-purified VLPs sample. VLP ultra-purification generally done using CsCl density-gradient ultracentrifugation. Additionally, important VLP-fraction treated DNase remove free DNA! sequencing, reads whole-community fraction assembled whole-community VLP-fraction reads mapped assembly. Read mapping performed using high minimum identity (0.97 higher) random mapping ambiguous reads. pileup files needed TrIdent generated using .bam files produced read mapping. Deep sequencing whole-community VLP-fractions needed transductomics! Sample preparation, sequencing procedures, bioinformatics methods detailed Kleiner et al.(2020).","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"pileup-files","dir":"Articles","previous_headings":"Input Data","what":"Pileup files","title":"TrIdent","text":"TrIdent detects read coverage patterns using pattern-matching algorithm operates pileup files. pileup file file format row summarizes ‘pileup’ reads specific genomic locations. Pileup files can used generate rolling mean read coverages associated base pair positions across metagenome assembly reduces data size preserving read coverage patterns. TrIdent requires input pileups files generated using 100 bp window/bin size. read mappers, like BBMap, allow generation pileup files bbmap.sh command use bincov output covbinsize=100 parameter/argument. Otherwise, BBMap’s pileup.sh can convert .bam files produced read mapper pileup files compatible TrIdent using bincov output binsize=100. TrIdent requires two pileup files transductomics dataset input: VLP-fraction pileup: Sequencing reads sample’s ultra-purified VLP-fraction mapped sample’s whole-community metagenome assembly. whole-community pileup: Sequencing reads sample’s whole-community mapped sample’s whole-community metagenome assembly. Remember- data used pileup file must originate sample. Pileup files must use 100 bp window/bin size rolling mean. input pileup files must following format: Dataframe four columns: V1: Contig accession V2: Mapped read coverage values averaged 100 bp windows V3: Starting position (bp) 100 bp window. Restarts 0 start new contig. V4: Starting position (bp) 100 bp window. restart start new contig.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"tridentclassifier","dir":"Articles","previous_headings":"","what":"TrIdentClassifier()","title":"TrIdent","text":"TrIdentClassifier() main function TrIdent. function filters contigs based length read coverage, performs pattern-matching classify contigs, identifies highly active/abundant heterogenously integrated Prophage-like elements, determines contigs high VLP-fraction:whole-community read coverage ratios, identifies start stop positions sizes pattern-matches, calculates slopes Sloping pattern-matches. Note TrIdentClassifier() results taken face value manual curation needed! recommend careful examination output plots determine agree TrIdentClassifier() classifications.","code":""},{"path":[]},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"contig-filtering","dir":"Articles","previous_headings":"TrIdentClassifier() > Function components","what":"Contig filtering","title":"TrIdent","text":"Contigs short little read coverage filtered prior pattern-matching. TrIdentClassifier() filters contigs least 10x coverage total 5,000 bp across whole contig. read coverage filtering done way avoid filtering long contigs short Prophage-like patterns might get removed filtering done read coverage averages medians. Additionally, contigs less 30,000 bp filtered default, however can changed minContigLength parameter. contigs shorter 30,000 bp may poor quality often long enough capture complete transduction patterns, allow users set minimum minContigLength 25,000 bp. like reduce size input pileup files TrIdent, consider pre-filtering assembly contigs greater 25,000 bp prior read mapping! expected majority contigs dataset filtered due low read coverage step! contigs filtered due low read coverage, may indication DNA contamination VLP-fraction.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"changing-pileup-windowsize","dir":"Articles","previous_headings":"TrIdentClassifier() > Function components","what":"Changing pileup windowSize","title":"TrIdent","text":"input pileup files 100 bp windows mapped read coverage averaged . small window size needed detect read coverage patterns associated specialized transduction may span thousand basepairs. However, read coverage patterns associated types transduction generally don’t require resolution 100 bp windows provide. users can use 100 bp windowSize TrIdentClassifier(), processing time increased significantly noisy data may interfere pattern-matching. find default 1,000 bp windowSize provides nice balance processing time read coverage pattern resolution.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"pattern-matching","dir":"Articles","previous_headings":"TrIdentClassifier() > Function components","what":"Pattern-matching","title":"TrIdent","text":"TrIdentClassifier() detects read coverage patterns VLP-fraction using pattern-matching approach. Several predefined patterns, described , built using specific length read coverage values contig assessed. Patterns translated across contig 1,000 bp sliding windows translation, pattern-match score calculated taking mean absolute difference VLP-fraction read coverage pattern values. smaller match-score, better pattern-match. pattern fully translated across contig, certain aspects pattern changed (.e. height, width, slope) translation repeated. process translation pattern re-scaling repeated large number pattern variations tested. pattern-matching complete, pattern associated best match-score used contig classification. Contigs classified ‘Prophage-like’, ‘Sloping’, ‘NoPattern’ pattern-matching.","code":""},{"path":[]},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"sloping","dir":"Articles","previous_headings":"","what":"TrIdent","title":"TrIdent","text":"four sloping pattern variations sloping pattern class. sloping patterns representative large DNA transfers take place generalized, lateral gene transfer agent (GTA) transduction due decreasing frequency DNA packaging moving away packaging initiation sites. pattern-matching, slope values sloping patterns decreased minimum slope 0.001 (change 10x read coverage 10,000 bp) reached. minimum slope value can changed minSlope parameter. Generalized, lateral GTA transduction events can span tens hundreds kilobasepairs DNA single contig typically capture entire event. Depending part transducing event captured contig, sloping can severe almost 0. Patterns 1 2 represent contigs capture Sloping transducing event somewhere middle DNA transfer. Patterns 2 4 represent contigs capture jump read coverage associated packaging initiation site Sloping transducing event. Patterns 2 4 translated across contig addition slopes changed slopes changed patterns 1 2.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"prophage-like","dir":"Articles","previous_headings":"","what":"TrIdent","title":"TrIdent","text":"three block patterns Prophage-like pattern class. block patterns representative integrated genetic elements can excised host chromosome mobilized. blocks read coverage define classification formed reads mobilized genetic elements packaged VLPs map back respective integration sites host bacterium’s chromosome. Prophage, phage-inducible chromosomal islands (PICIs), transposons examples genetic elements fall Prophage-like class. pattern-matching, heights widths block patterns altered pattern variations translated across contig. block pattern widths never get smaller 10,000 bp default, however can changed minBlockSize parameter. Pattern 1 represents Prophage-like element entirely contig patterns 2 3 represent Prophage-like elements trail right left side contig, respectively. Prophage-like classification example transduction , may transduction associated Prophage-like classifications. improper excision Prophage-like elements may lead specialized transduction genes neighboring element’s integration site. TrIdent’s specializedTransductionID() function (explained detail ) attempt detect specialized transduction events associated Prophage-like classifications.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"nopattern","dir":"Articles","previous_headings":"","what":"TrIdent","title":"TrIdent","text":"Since best pattern-match contig determined comparing match-scores amongst pattern-variations pattern classes, needed ‘negative control’ pattern compare . ‘NoPattern’ ‘pattern’ serves negative control matching contigs read coverage patterns. made two NoPattern patterns consist horizontal line length contig assessed either average median read coverage contig. pattern re-scaled translated way. Note read coverage patterns heavily dependent depth read coverage achieved sequencing therefore rare transduction events may achieve sufficient read coverage detection read coverage pattern-matching. Rather label contigs read coverage pattern ‘transduction’, instead label ‘pattern’.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"highly-activeabundant-and-heterogenously-integratedpresent-prophage-like-elements","dir":"Articles","previous_headings":"TrIdentClassifier() > Function components","what":"Highly active/abundant and heterogenously integrated/present Prophage-like elements","title":"TrIdent","text":"Prophage-like elements actively replicating highly abundant typically generate sequencing reads rest host bacterium’s chromosome. may create region elevated read coverage element’s insertion site whole-community fraction read coverage. Conversely, Prophage-like element integrated portion host bacterial population, may dip depression read coverage integration site whole-community read coverage. order determine whole-community read coverage elevated depressed site Prophage-like element, one must know Prophage-like element’s genomic location. tools rely annotation information identify Prophage-like elements whole-community metagenomes, TrIdentClassifier() uses VLP-fraction read coverage patterns. locations Prophage-like pattern-matches used calculate Prophage-like:non-Prophage-like whole-community read coverage ratio. Prophage-like patterns whole-community read coverage ratios greater 1.15 labeled ‘elevated’ ratios less 0.75 labeled ‘depressed’.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"nopattern-classifications-with-high-vlp-fractionwhole-community-read-coverage-ratios","dir":"Articles","previous_headings":"TrIdentClassifier() > Function components","what":"NoPattern classifications with high VLP-fraction:whole-community read coverage ratios","title":"TrIdent","text":"contig receives noPattern classification, proceeds additional classification step either leaves classification re-classifies contig high VLP-fraction:whole-community read coverage ratio (‘HighCovNoPattern’). words, contigs HighCovNoPattern classification even read coverage across contig (.e. notable read coverage pattern) VLP-fraction read coverage notably higher whole-community read coverage. re-classification necessary certain biologically significant events may interest user can characteristics. First, certain transduction events, specifically associated Sloping classification, may long extend across multiple contigs. ‘tails’ sloping patterns created events may little actual sloping (pattern) relatively high read coverage (Fig S2 Kleiner et al., 2020). Second, evidence membrane vesicle (MV) mediated transduction (also known vesiduction protected extracellular transformation) produces relatively even read coverage patterns purified MV sequencing reads mapped back bacterial chromosome origin (Faddetta et al., 2022). Lastly, phage genomes assembled contigs whole-community fraction may generate high levels even read coverage phage reads VLP-fraction map back genome sequences. Contigs median VLP-fraction:Whole-community read coverage ratios greater 2, words contigs median VLP-fraction read coverage value 2x whole-community median read coverage value, re-classified HighCovNoPattern. Reference: Faddetta, T., Vassallo, ., Del Duca, S. et al. Unravelling DNA sequences carried Streptomyces coelicolor membrane vesicles. Sci Rep 12, 16651 (2022). https://doi.org/10.1038/s41598-022-21002-z","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"usage","dir":"Articles","previous_headings":"TrIdentClassifier()","what":"Usage","title":"TrIdent","text":"Default arguments:","code":"TrIdentOutput <- TrIdentClassifier(   VLPpileup = VLPFractionSamplePileup,   WCpileup = WholeCommunitySamplePileup ) #> Reformatting pileup files #> Starting pattern-matching... #> A quarter of the way done with pattern-matching #> Half of the way done with pattern-matching #> Almost done with pattern-matching! #> Determining sizes (bp) of pattern matches #> Identifying highly active/abundant or heterogenously integrated #>         Prophage-like elements #> Finalizing output #> Execution time: 14.75secs #> 1 contigs were filtered out based on low read coverage #> 0 contigs were filtered out based on length #>  #> HighCovNoPattern        NoPattern    Prophage-like          Sloping  #>                1                1                4                3 #> 3 of the prophage-like classifications are highly active or abundant #> 1 of the prophage-like classifications are mixed, i.e. heterogenously #>         integrated into their bacterial host population"},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"argumentsparameters","dir":"Articles","previous_headings":"TrIdentClassifier()","what":"Arguments/Parameters","title":"TrIdent","text":"VLPpileup: VLP-fraction pileup file. WCpileup: Whole-community pileup file. windowSize: number basepairs average read coverage values . Options 100, 200, 500, 1000 . Default 1000. minBlockSize: minimum size (bp) Prophage-like block pattern. Default 10000. Must greater 1000. maxBlockSize: maximum size (bp) Prophage-like block pattern. Default NA (maximum). minContigLength: minimum contig size (bp) perform pattern-matching . Must least 25000. Default 30000. minSlope: minimum slope value test sloping patterns. Default 0.001 (.e minimum change 10x read coverage 100,000 bp). suggFiltThresh: TRUE FALSE, Suggest filtering threshold TrIdent classifications based normalized pattern-match scores. Default FALSE. SaveFilesTo: Optional, Provide path directory wish save output . folder made within provided directory store results.","code":"TrIdentClassifier(VLPpileup, WCpileup,   windowSize = 1000, minBlockSize = 10000,   maxBlockSize = Inf, minContigLength = 30000, minSlope = 0.001,   suggFiltThresh = FALSE, SaveFilesTo )"},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"output","dir":"Articles","previous_headings":"TrIdentClassifier()","what":"Output","title":"TrIdent","text":"TrIdentClassifier() outputs histogram displaying overall abundance quality pattern-matches addition composition classifications. displayed pattern-match scores normalized dividing score associated contig length. scores normalized visualize overall quality pattern-matching entire dataset. Remember, smaller pattern-match scores correspond better pattern-matches. output TrIdentClassifier() list containing five objects: SummaryTable: table containing classification information contigs filtered . CleanedSummaryTable: cleaned summary table containing classification information contigs classified Prophage-like, Sloping HighCovNoPattern. PatternMatchInfo: list pattern-match information used functions TrIdent. FilteredOutContigTable: table containing contigs filtered reason (low read coverage short). windowSize: windowSize used. Save desired list-item new variable using associated name. Summary table:","code":"TrIdentSummaryTable <- TrIdentOutput$SummaryTable"},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"plottridentresults","dir":"Articles","previous_headings":"","what":"plotTrIdentResults()","title":"TrIdent","text":"plotTrIdentResults() allows users visualize whole-community VLP-fraction read coverage pattern-match associated contig classified Prophage-like, Sloping HighCovNoPattern.","code":""},{"path":[]},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"re-building-pattern-matches","dir":"Articles","previous_headings":"plotTrIdentResults() > Function components","what":"Re-building pattern-matches","title":"TrIdent","text":"TrIdentClassifier() output contains information needed re-build pattern-match used contig classification. re-build complete pattern-match visualization, plotTrIdentResults() uses pattern-match’s minimum maximum values start stop positions.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"plotting-read-coverage-and-associated-pattern-matches","dir":"Articles","previous_headings":"plotTrIdentResults() > Function components","what":"Plotting read coverage and associated pattern-matches","title":"TrIdent","text":"whole-community VLP-fraction read coverage plotted contig classified Prophage-like, Sloping HighCovNoPattern. pattern-match associated classification overlaid VLP-fraction read coverage. whole-community read coverage displayed visualization elevated depressed Prophage-like region read coverage.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"usage-1","dir":"Articles","previous_headings":"plotTrIdentResults()","what":"Usage","title":"TrIdent","text":"Default arguments:","code":"TrIdentPlots <- plotTrIdentResults(   VLPpileup = VLPFractionSamplePileup,   WCpileup = WholeCommunitySamplePileup,   TrIdentResults = TrIdentOutput )"},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"argumentsparameters-1","dir":"Articles","previous_headings":"plotTrIdentResults()","what":"Arguments/Parameters","title":"TrIdent","text":"VLPpileup: VLP-fraction pileup file. WCpileup: Whole-community pileup file. TrIdentResults: output TrIdentClassifier() matchScoreFilter: Optional, Filter plots using normalized pattern match-scores. suggested filtering threshold provided TrIdentClassifier() suggFiltThresh=TRUE. saveFilesTo: Optional, Provide path directory wish save output . folder made within provided directory store results.","code":"plotTrIdentResults(   VLPpileup, WCpileup, TrIdentResults, matchScoreFilter,   saveFilesTo )"},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"output-1","dir":"Articles","previous_headings":"plotTrIdentResults()","what":"Output","title":"TrIdent","text":"output plotTrIdentResults() list containing ggplot objects. list contains read coverage plots contigs classified Sloping, Prophage-like, HighCovNoPattern respective pattern-matches. default, plots displayed raw read coverage values. recommend users also view plots using logScale=TRUE specialized transduction patterns occur low frequencies can visualized using log scaled read coverage values. View plots:  View one plot:","code":"TrIdentPlots TrIdentPlots$NODE_62"},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"specializedtransductionid","dir":"Articles","previous_headings":"","what":"specializedTransductionID()","title":"TrIdent","text":"Specialized transduction occurs integrated Prophage-like element excises packages small portion bacterial DNA directly outside borders insertion site. specializedTransductionID() searches contigs classified Prophage-like dense read coverage outside borders Prophage-like patterns might represent specialized transduction events. specialized transduction tends fairly short (couple kbps) compared generalized, lateral GTA transduction (tens hundreds kbps), averaging read coverage 1,000 bp distance (.e using windowSize=1000) can ‘blur’ specialized transduction patterns. specialized transduction identified TrIdentClassifier(). Instead, use locations Prophage-like elements identified TrIdentClassifier() guide search specialized transduction specializedTransductionID(). Note specializedTransductionID() results taken face value manual curation needed! recommend careful examination output plots determine agree specializedTransductionID() results. Setting logScale=TRUE plot read coverage log10 scale may help visualization low-frequency specialized transduction events. aware cases, log scaled read coverage can obfuscate Prophage-like element pattern .","code":""},{"path":[]},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"zoom-in-on-prophage-like-elements","dir":"Articles","previous_headings":"specializedTransductionID() > Function components","what":"Zoom-in on Prophage-like elements","title":"TrIdent","text":"Since, specialized transduction read coverage patterns relatively small, specializedTransductionID() ‘zooms-’ Prophage-like elements aid specialized transduction visualization. ‘zoom-’ Prophage-like elements, specializedTransductionID() uses pattern-match information generated TrIdentClassifier() subset contig 50,000 bp outside pattern-match borders.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"identify-borders-of-prophage-like-elements","dir":"Articles","previous_headings":"specializedTransductionID() > Function components","what":"Identify borders of Prophage-like elements","title":"TrIdent","text":"Since windowSize used pattern-matching TrIdentClassifier() likely larger 100 bp, Prophage-like pattern-match border locations directly translate border locations 100 bp windowSize. re-identify borders Prophage-like elements, use rolling standard deviation (SD) detect large changes read coverage associated Prophage-like element borders. First, contig subset surrounding left right pattern-match borders. contigs Prophage-like pattern-match trails side contig, border falls contig subset. Next, subset, rolling SD calculated read coverage value contig position associated largest SD chosen border location. border locations marked output plots black vertical lines.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"search-for-specialized-transduction-outside-prophage-like-borders","dir":"Articles","previous_headings":"specializedTransductionID() > Function components","what":"Search for specialized transduction outside Prophage-like borders","title":"TrIdent","text":"Prophage-like element borders identified, specializedTransductionID() starts border locations searches outwards dense read coverage meet ‘requirements’ specialized transduction defined two parameters specializedTransductionID(): noReadCov specTransLength specializedTransductionID() first makes sure coverage detects outside borders disrupted defined region read coverage (noReadCov). default value noReadCov 500 bp. Secondly, specializedTransductionID ensures read coverage detects outside Prophage-like borders meets minimum length requirement (specTransLength). default value specTransLength 2000 bp. default, specializedTransductionID() search coverage directly outside Prophage-like borders least 2000 bp long interrupted point 500 bp read coverage. requirements met, specializedTransductionID() label contig specialized transduction. ‘end’ specialized transduction region marked output plots red vertical lines. Additionally, read coverage plots contigs specialized transduction colored green instead blue.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"usage-2","dir":"Articles","previous_headings":"specializedTransductionID()","what":"Usage","title":"TrIdent","text":"Default arguments:","code":"SpecTransduc <- specializedTransductionID(   VLPpileup = VLPFractionSamplePileup,   TrIdentResults = TrIdentOutput ) #> 2 contigs have potential specialized transduction #> We recommend that you also view the results of this search with #>       logScale=TRUE"},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"argumentsparameters-2","dir":"Articles","previous_headings":"specializedTransductionID()","what":"Arguments/Parameters","title":"TrIdent","text":"VLPpileup: VLP-fraction pileup file. TrIdentResults: output TrIdentClassifier(). noReadCov: Number basepairs zero read coverage encountered specialized transduction searching stops. Default 500. Must least 100. specTransLength: Number basepairs non-zero read coverage needed specialized transduction considered. Default 2000. Must least  logScale: TRUE FALSE, display VLP-fraction read coverage log10 scale. Default FALSE. matchScoreFilter: Optional, Filter plots using normalized pattern match-scores. suggested filtering threshold provided TrIdentClassifier() suggFiltThresh=TRUE. SaveFilesTo: Optional, Provide path directory wish save output . folder made within provided directory store results. specificContig: Optional, Search specific contig classified Prophage-like (“NODE_1”).","code":"specializedTransductionID(VLPpileup, TrIdentResults,   noReadCov = 500, specTransLength = 2000,   logScale = FALSE, matchScoreFilter,   SaveFilesTo, specificContig )"},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"output-2","dir":"Articles","previous_headings":"specializedTransductionID()","what":"Output","title":"TrIdent","text":"output specializedTransductionID() list containing two objects: summaryTable: table containing specializedTransductionID() results contigs classified Prophage-like TrIdentClassifier(). Plots: list ggplot objects contigs classified Prophage-like. plots ‘zoomed-’ Prophage-like pattern aid specialized transduction visualization. Prophage-like element borders identified specializedTransductionID() marked plot black vertical lines. specializedTransductionID() identifies potential specialized transduction, plot colored green instead blue. end specialized transduction marked red vertical line. Save desired list-item new variable using associated name. Summary table: View plots:  View specific plot:","code":"SpecializedTransducSummaryTable <- SpecTransduc$summaryTable SpecTransduc$Plots SpecTransduc$Plots$NODE_62"},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"generate-final-trident-summary-table","dir":"Articles","previous_headings":"","what":"Generate final TrIdent summary table","title":"TrIdent","text":"’d like combine summary tables produced TrIdentClassifier() specializedTransductionID(), try following:","code":"FinalTrIdentSummaryTable <- merge(TrIdentSummaryTable,   SpecializedTransducSummaryTable,   by = \"contigName\", all.x = TRUE )"},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"session-information","dir":"Articles","previous_headings":"","what":"Session Information","title":"TrIdent","text":"","code":"sessionInfo() #> R version 4.2.1 (2022-06-23 ucrt) #> Platform: x86_64-w64-mingw32/x64 (64-bit) #> Running under: Windows 10 x64 (build 19045) #>  #> Matrix products: default #>  #> locale: #> [1] LC_COLLATE=English_United States.utf8  #> [2] LC_CTYPE=English_United States.utf8    #> [3] LC_MONETARY=English_United States.utf8 #> [4] LC_NUMERIC=C                           #> [5] LC_TIME=English_United States.utf8     #>  #> attached base packages: #> [1] stats     graphics  grDevices utils     datasets  methods   base      #>  #> other attached packages: #> [1] kableExtra_1.4.0   ggplot2_3.5.1      patchwork_1.3.0    knitr_1.49         #> [5] TrIdent_0.0.0.9000 #>  #> loaded via a namespace (and not attached): #>  [1] Rcpp_1.0.13-1      bslib_0.8.0        compiler_4.2.1     pillar_1.9.0       #>  [5] jquerylib_0.1.4    tools_4.2.1        digest_0.6.37      viridisLite_0.4.2  #>  [9] jsonlite_1.8.9     evaluate_1.0.1     lifecycle_1.0.4    tibble_3.2.1       #> [13] gtable_0.3.6       pkgconfig_2.0.3    rlang_1.1.4        cli_3.6.2          #> [17] rstudioapi_0.17.1  roll_1.1.7         yaml_2.3.10        pkgdown_2.1.1      #> [21] xfun_0.49          fastmap_1.2.0      xml2_1.3.6         withr_3.0.2        #> [25] stringr_1.5.1      dplyr_1.1.4        generics_0.1.3     desc_1.4.3         #> [29] fs_1.6.5           vctrs_0.6.5        htmlwidgets_1.6.4  sass_0.4.9         #> [33] systemfonts_1.1.0  grid_4.2.1         tidyselect_1.2.1   svglite_2.1.3      #> [37] glue_1.8.0         R6_2.5.1           textshaping_0.4.1  fansi_1.0.6        #> [41] rmarkdown_2.29     purrr_1.0.2        tidyr_1.3.1        farver_2.1.2       #> [45] magrittr_2.0.3     scales_1.3.0       htmltools_0.5.8.1  colorspace_2.1-1   #> [49] labeling_0.4.3     ragg_1.3.3         utf8_1.2.4         stringi_1.8.4      #> [53] RcppParallel_5.1.9 munsell_0.5.1      cachem_1.1.0"},{"path":"https://jlmaier12.github.io/TrIdent/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Jessie Maier. Author, maintainer, copyright holder. Jorden Rabasco. Author, contributor. Craig Gin. Author. Benjamin Callahan. Author. Manuel Kleiner. Author, thesis advisor.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Maier J, Rabasco J, Gin C, Callahan B, Kleiner M (2024). TrIdent: Detect Genetic Transduction Events Metagenomes using Read Coverage Pattern-Matching. https://github.com/jlmaier12/TrIdent, https://jlmaier12.github.io/TrIdent/.","code":"@Manual{,   title = {TrIdent: Detect Genetic Transduction Events in Metagenomes using Read Coverage Pattern-Matching},   author = {Jessie Maier and Jorden Rabasco and Craig Gin and Benjamin Callahan and Manuel Kleiner},   year = {2024},   note = {https://github.com/jlmaier12/TrIdent, https://jlmaier12.github.io/TrIdent/}, }"},{"path":"https://jlmaier12.github.io/TrIdent/index.html","id":"trident","dir":"","previous_headings":"","what":"Detect Genetic Transduction Events in Metagenomes using Read Coverage Pattern-Matching","title":"Detect Genetic Transduction Events in Metagenomes using Read Coverage Pattern-Matching","text":"TrIdent automates analysis transductomics data detecting, classifying, characterizing read coverage patterns associated potential transduction events. Transductomics, developed Kleiner et al. (2020), DNA sequencing-based method detection characterization transduction events pure cultures complex communities. Transductomics relies mapping sequencing reads viral-like particle (VLP)-fraction sample contigs assembled metagenome (whole-community) sample. Reads bacterial DNA carried VLPs map back bacterial contigs origin creating read coverage patterns indicative ongoing transduction. read coverage patterns detected represent DNA actively carried transduced VLPs. read coverage patterns represent complete transduction events (.e integration transduced DNA new bacterial chromosomes). obtain data needed transductomics, microbiome sample interest split prepare two sub-sample types: - Whole-community: Represents ‘whole-community’ (bacteria, fungi, virus, etc) microbiome interest - VLP-fraction: Represents virus ‘viral-like particles’ associated microbiome interest - VLP-fraction must obtained appropriate ultra-purification protocol sample type remove bacterial cells contaminating free bacterial DNA. transductomics TrIdent, researcher can obtain information phage-host pairs involved transduction, types transduction occuring, region host genome potentially transduced, allows exploration transferred genes. Reference: Kleiner, M., Bushnell, B., Sanderson, K.E. et al. Transductomics: sequencing-based detection analysis transduced DNA pure cultures microbial communities. Microbiome 8, 158 (2020). https://doi.org/10.1186/s40168-020-00935-5","code":""},{"path":"https://jlmaier12.github.io/TrIdent/index.html","id":"input-files","dir":"","previous_headings":"","what":"Input files","title":"Detect Genetic Transduction Events in Metagenomes using Read Coverage Pattern-Matching","text":"TrIdent detects read coverage patterns using pattern-matching algorithm operates pileup files. pileup file file format row summarizes ‘pileup’ reads specific genomic locations. Pileup files can used generate rolling mean read coverages associated base pair positions across metagenome assembly reduces data size preserving read coverage patterns. TrIdent requires input pileups files generated using 100 bp window/bin size. read mappers, like BBMap, allow generation pileup files bbmap.sh command use bincov output covbinsize=100 parameter/argument. Otherwise, BBMap’s pileup.sh can convert .bam files produced read mapper pileup files compatible TrIdent using bincov output binsize=100. TrIdent requires two pileup files transductomics dataset input: VLP-fraction pileup: Sequencing reads sample’s ultra-purified VLP-fraction mapped whole-community metagenome assembly sample. whole-community pileup: Sequencing reads sample’s whole-community mapped whole-community metagenome sample. data used pileup file must originate sample. Pileup files must use 100 bp window/bin size rolling mean. Transductomics sample preparation, sequencing procedures, analysis methods detailed Kleiner et al. (2020)","code":""},{"path":"https://jlmaier12.github.io/TrIdent/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Detect Genetic Transduction Events in Metagenomes using Read Coverage Pattern-Matching","text":"can install development version TrIdent GitHub :","code":"# install.packages(\"pak\") pak::pak(\"jlmaier12/TrIdent\")"},{"path":"https://jlmaier12.github.io/TrIdent/index.html","id":"quick-start","dir":"","previous_headings":"","what":"Quick Start","title":"Detect Genetic Transduction Events in Metagenomes using Read Coverage Pattern-Matching","text":"","code":"library(TrIdent)  ## Run first TrIdentOutput <- TrIdentClassifier(   VLPpileup = VLPFractionSamplePileup,   WCpileup = WholeCommunitySamplePileup ) #> Reformatting pileup files #> Starting pattern-matching... #> A quarter of the way done with pattern-matching #> Half of the way done with pattern-matching #> Almost done with pattern-matching! #> Determining sizes (bp) of pattern matches #> Identifying highly active/abundant or heterogenously integrated #>         Prophage-like elements #> Finalizing output #> Execution time: 14.56secs #> 1 contigs were filtered out based on low read coverage #> 0 contigs were filtered out based on length #>  #> HighCovNoPattern        NoPattern    Prophage-like          Sloping  #>                1                1                4                3 #> 3 of the prophage-like classifications are highly active or abundant #> 1 of the prophage-like classifications are mixed, i.e. heterogenously #>         integrated into their bacterial host population ## Run second TrIdentPlots <- plotTrIdentResults(   VLPpileup = VLPFractionSamplePileup,   WCpileup = WholeCommunitySamplePileup,   TrIdentResults = TrIdentOutput )  ## Run third SpecTransduc <- specializedTransductionID(   VLPpileup = VLPFractionSamplePileup,   TrIdentResults = TrIdentOutput ) #> 2 contigs have potential specialized transduction #> We recommend that you also view the results of this search with #>       logScale=TRUE"},{"path":"https://jlmaier12.github.io/TrIdent/reference/allPatternMatches.html","id":null,"dir":"Reference","previous_headings":"","what":"Collects pattern-match information for all classifications — allPatternMatches","title":"Collects pattern-match information for all classifications — allPatternMatches","text":"Collects pattern information associated contigs classified Prophage-like, Sloping HighCovNoPattern.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/allPatternMatches.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collects pattern-match information for all classifications — allPatternMatches","text":"","code":"allPatternMatches(bestMatchList, classifSummTable)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/allPatternMatches.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collects pattern-match information for all classifications — allPatternMatches","text":"bestMatchList Classifications made patternMatcher function. classifSummTable Classification summary table whole-community:VLP-fraction read coverage ratios calculated.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/allPatternMatches.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collects pattern-match information for all classifications — allPatternMatches","text":"List","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/allProphageLikeClassifs.html","id":null,"dir":"Reference","previous_headings":"","what":"Collects Prophage-like classification pattern-match information — allProphageLikeClassifs","title":"Collects Prophage-like classification pattern-match information — allProphageLikeClassifs","text":"Collects pattern information associated contigs classified Prophage-like.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/allProphageLikeClassifs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collects Prophage-like classification pattern-match information — allProphageLikeClassifs","text":"","code":"allProphageLikeClassifs(bestMatchList)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/allProphageLikeClassifs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collects Prophage-like classification pattern-match information — allProphageLikeClassifs","text":"bestMatchList Classifications made patternMatcher function.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/allProphageLikeClassifs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collects Prophage-like classification pattern-match information — allProphageLikeClassifs","text":"List","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/allSlopingClassifs.html","id":null,"dir":"Reference","previous_headings":"","what":"Collects Sloping classification pattern-match i nformation — allSlopingClassifs","title":"Collects Sloping classification pattern-match i nformation — allSlopingClassifs","text":"Collects pattern information associated contigs classified Sloping patternMatcher function.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/allSlopingClassifs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collects Sloping classification pattern-match i nformation — allSlopingClassifs","text":"","code":"allSlopingClassifs(bestMatchList)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/allSlopingClassifs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collects Sloping classification pattern-match i nformation — allSlopingClassifs","text":"bestMatchList Classifications made patternMatcher function.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/allSlopingClassifs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collects Sloping classification pattern-match i nformation — allSlopingClassifs","text":"List","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/blockBuilder.html","id":null,"dir":"Reference","previous_headings":"","what":"Builds prophage-like block patterns — blockBuilder","title":"Builds prophage-like block patterns — blockBuilder","text":"Build translate block pattern going left side, right side full length contig.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/blockBuilder.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Builds prophage-like block patterns — blockBuilder","text":"","code":"blockBuilder(viralSubset, windowSize, minBlockSize, maxBlockSize)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/blockBuilder.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Builds prophage-like block patterns — blockBuilder","text":"viralSubset subset read coverage pileup pertains contig currently assessed windowSize window size used re-average read coverage pileups minBlockSize minimum size prophage-like block pattern. Default 10000 bp. maxBlockSize maximum size prophage-like block pattern. Default NA.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/blockBuilder.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Builds prophage-like block patterns — blockBuilder","text":"List containing three objects","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/blockTranslator.html","id":null,"dir":"Reference","previous_headings":"","what":"Full block pattern-translator — blockTranslator","title":"Full block pattern-translator — blockTranslator","text":"Translates full block-pattern across contig. Translate pattern 1000 bp time. Stop translating pattern 5000 bp end contig.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/blockTranslator.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Full block pattern-translator — blockTranslator","text":"","code":"blockTranslator(viralSubset, bestMatchInfo, windowSize, pattern)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/blockTranslator.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Full block pattern-translator — blockTranslator","text":"viralSubset subset read coverage pileup pertains contig currently assessed bestMatchInfo information associated current best pattern-match. windowSize window size used re-average read coverage pileups pattern vector containing values associated block pattern","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/blockTranslator.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Full block pattern-translator — blockTranslator","text":"List","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/changeSlope.html","id":null,"dir":"Reference","previous_headings":"","what":"Change slope of sloping pattern — changeSlope","title":"Change slope of sloping pattern — changeSlope","text":"Change value slope used sloping pattern-match","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/changeSlope.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Change slope of sloping pattern — changeSlope","text":"","code":"changeSlope(   leftOrRight,   slopeBottom,   halfToMaxReadCov,   cov,   viralSubset,   windowSize )"},{"path":"https://jlmaier12.github.io/TrIdent/reference/changeSlope.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Change slope of sloping pattern — changeSlope","text":"leftOrRight Generate pattern negative slope (left right, .e. 'Left') positive slope (right left, .e. 'Right') slopeBottom value bottom sloping value halfToMaxReadCov Half max VLP-fraction read coverage divided 10 cov value top slope viralSubset subset read coverage pileup pertains contig currently assessed windowSize window size used re-average read coverage pileup","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/changeSlope.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Change slope of sloping pattern — changeSlope","text":"List","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/changeSlopeWStart.html","id":null,"dir":"Reference","previous_headings":"","what":"Change slope of sloping pattern with initial start — changeSlopeWStart","title":"Change slope of sloping pattern with initial start — changeSlopeWStart","text":"Change value slope used sloping start pattern-match","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/changeSlopeWStart.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Change slope of sloping pattern with initial start — changeSlopeWStart","text":"","code":"changeSlopeWStart(   leftOrRight,   slopeBottom,   slopeBottomChange,   cov,   viralSubset,   windowSize )"},{"path":"https://jlmaier12.github.io/TrIdent/reference/changeSlopeWStart.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Change slope of sloping pattern with initial start — changeSlopeWStart","text":"leftOrRight Generate pattern negative slope (left right, .e. 'Left') positive slope (right left, .e. 'Right') slopeBottom value bottom sloping value slopeBottomChange value used increase bottom slope cov value top slope viralSubset subset read coverage pileup pertains contig currently assessed windowSize window size used re-average read coverage pileup","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/changeSlopeWStart.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Change slope of sloping pattern with initial start — changeSlopeWStart","text":"List","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/changeWindowSize.html","id":null,"dir":"Reference","previous_headings":"","what":"Change the read coverage rolling mean window size — changeWindowSize","title":"Change the read coverage rolling mean window size — changeWindowSize","text":"Re-averages window sizes read coverage averages. Start 100bp windows always. make window size less 100bp.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/changeWindowSize.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Change the read coverage rolling mean window size — changeWindowSize","text":"","code":"changeWindowSize(cleanPileup, windowSize)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/changeWindowSize.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Change the read coverage rolling mean window size — changeWindowSize","text":"cleanPileup read coverage dataset cleaned reformatted. windowSize number base pairs average coverage values . Options 100, 500, 1000, 2000 !","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/changeWindowSize.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Change the read coverage rolling mean window size — changeWindowSize","text":"Dataframe","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/contigClassSumm.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarizes pattern-match information — contigClassSumm","title":"Summarizes pattern-match information — contigClassSumm","text":"Summarizes classifications made patternMatcher() function dataframe.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/contigClassSumm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarizes pattern-match information — contigClassSumm","text":"","code":"contigClassSumm(bestMatchList)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/contigClassSumm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarizes pattern-match information — contigClassSumm","text":"bestMatchList Classifications made patternMatcher function.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/contigClassSumm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarizes pattern-match information — contigClassSumm","text":"dataframe","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/fullSlope.html","id":null,"dir":"Reference","previous_headings":"","what":"Sloping pattern builder — fullSlope","title":"Sloping pattern builder — fullSlope","text":"Build sloping pattern consists sloping line spanning contig assessed. line slopes left right. slope line changed, pattern translated across contig.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/fullSlope.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sloping pattern builder — fullSlope","text":"","code":"fullSlope(viralSubset, windowSize, minSlope)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/fullSlope.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sloping pattern builder — fullSlope","text":"viralSubset subset read coverage pileup pertains contig currently assessed windowSize window size used re-average read coverage pileup minSlope minimum slope value test sloping patterns","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/fullSlope.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sloping pattern builder — fullSlope","text":"List containing two objects","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/leftRightBlockTranslater.html","id":null,"dir":"Reference","previous_headings":"","what":"Translate left and right block patterns across contig — leftRightBlockTranslater","title":"Translate left and right block patterns across contig — leftRightBlockTranslater","text":"Translates left right block patterns across contigs 1000 bp time","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/leftRightBlockTranslater.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Translate left and right block patterns across contig — leftRightBlockTranslater","text":"","code":"leftRightBlockTranslater(   viralSubset,   pattern,   leftOrRight,   windowSize,   minReadCov,   cov,   bestMatchInfo,   minBlockSize )"},{"path":"https://jlmaier12.github.io/TrIdent/reference/leftRightBlockTranslater.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Translate left and right block patterns across contig — leftRightBlockTranslater","text":"viralSubset subset read coverage pileup pertains contig currently assessed pattern pattern vector translated leftOrRight left right block pattern translated windowSize window size used re-average read coverage pileups minReadCov baseline value used region outside block pattern (either 0 minimum VLP-fraction read coverage contig) cov height value currently used block pattern bestMatchInfo information associated current best pattern-match. minBlockSize minimum size Prophage-like block pattern. Default 10,000 bp.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/leftRightBlockTranslater.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Translate left and right block patterns across contig — leftRightBlockTranslater","text":"List","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/makeBlockPattern.html","id":null,"dir":"Reference","previous_headings":"","what":"Make block patterns for pattern-matching — makeBlockPattern","title":"Make block patterns for pattern-matching — makeBlockPattern","text":"Make full, left right block patterns Prophage-like classifications","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/makeBlockPattern.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make block patterns for pattern-matching — makeBlockPattern","text":"","code":"makeBlockPattern(   viralSubset,   windowSize,   fullLeftRight,   blockLength,   nonBlock,   minReadCov,   cov )"},{"path":"https://jlmaier12.github.io/TrIdent/reference/makeBlockPattern.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make block patterns for pattern-matching — makeBlockPattern","text":"viralSubset subset read coverage pileup pertains contig currently assessed windowSize window size used re-average read coverage pileups fullLeftRight block pattern variation built blockLength Maximum block pattern length nonBlock Maximum non-block pattern length minReadCov Either 0 minimum VLP-fraction read coverage value cov height value block pattern","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/makeBlockPattern.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make block patterns for pattern-matching — makeBlockPattern","text":"List containing two objects","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/makeFullSlopes.html","id":null,"dir":"Reference","previous_headings":"","what":"Make full slope patterns — makeFullSlopes","title":"Make full slope patterns — makeFullSlopes","text":"Makes slope patterns sloping either left right (Left) right left (right) across contig assessed.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/makeFullSlopes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make full slope patterns — makeFullSlopes","text":"","code":"makeFullSlopes(leftOrRight, viralSubset, newMax, minReadCov, windowSize)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/makeFullSlopes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make full slope patterns — makeFullSlopes","text":"leftOrRight Generate pattern negative slope (left right, .e. 'Left') positive slope (right left, .e. 'Right') viralSubset subset read coverage pileup pertains contig currently assessed newMax value top sloping pattern slightly higher maximum coverage value viralSubset minReadCov Minimum read coverage value viralSubset windowSize window size used re-average read coverage pileups","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/makeFullSlopes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make full slope patterns — makeFullSlopes","text":"List","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/makeSlopesWStarts.html","id":null,"dir":"Reference","previous_headings":"","what":"Make slope patterns with starts — makeSlopesWStarts","title":"Make slope patterns with starts — makeSlopesWStarts","text":"Makes slope patterns sloping either left right (Left) right left (right) across contig assessed. Slope patterns contain initiation point.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/makeSlopesWStarts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make slope patterns with starts — makeSlopesWStarts","text":"","code":"makeSlopesWStarts(leftOrRight, viralSubset, newMax, minReadCov, windowSize)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/makeSlopesWStarts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make slope patterns with starts — makeSlopesWStarts","text":"leftOrRight Generate pattern negative slope (left right, .e. 'Left') positive slope (right left, .e. 'Right') viralSubset subset read coverage pileup pertains contig currently assessed newMax value top sloping pattern slightly higher maximum coverage value viralSubset minReadCov Minimum read coverage value viralSubset windowSize window size used re-average read coverage pileup","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/makeSlopesWStarts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make slope patterns with starts — makeSlopesWStarts","text":"List","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/NARemover.html","id":null,"dir":"Reference","previous_headings":"","what":"NA remover — NARemover","title":"NA remover — NARemover","text":"Removes NAs dataframe.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/NARemover.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"NA remover — NARemover","text":"","code":"NARemover(x)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/NARemover.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"NA remover — NARemover","text":"x dataset potential NAs","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/NARemover.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"NA remover — NARemover","text":"Dataframe","code":""},{"path":[]},{"path":"https://jlmaier12.github.io/TrIdent/reference/noPattern.html","id":null,"dir":"Reference","previous_headings":"","what":"No pattern pattern-match — noPattern","title":"No pattern pattern-match — noPattern","text":"horizontal line mean median coverage optimal pattern-match contig read coverage displays sloping block patterns","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/noPattern.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"No pattern pattern-match — noPattern","text":"","code":"noPattern(viralSubset)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/noPattern.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"No pattern pattern-match — noPattern","text":"viralSubset subset read coverage pileup pertains contig currently assessed","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/noPattern.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"No pattern pattern-match — noPattern","text":"List","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/patternBuilder.html","id":null,"dir":"Reference","previous_headings":"","what":"Pattern-builder — patternBuilder","title":"Pattern-builder — patternBuilder","text":"Builds pattern (vector) associated best pattern-match' contig classified Prophage-like, Sloping, HighCovNoPattern.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/patternBuilder.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pattern-builder — patternBuilder","text":"","code":"patternBuilder(viralSubset, classifList, classification, i)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/patternBuilder.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pattern-builder — patternBuilder","text":"viralSubset subset read coverage pileup pertains contig currently assessed classifList list containing pattern match information associated classified contigs. classification contig's classification assigned TrIdentClassifier function list index associated contig's pattern-match information","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/patternBuilder.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pattern-builder — patternBuilder","text":"Vector","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/patternMatcher.html","id":null,"dir":"Reference","previous_headings":"","what":"Main pattern-matching function — patternMatcher","title":"Main pattern-matching function — patternMatcher","text":"Creates viralSubset, representative one contig, used input individual pattern-matching function. information associated best match pattern obtained, pattern smallest match score used classify contig assessed. Prior pattern-matching, contigs smaller minContigLength contigs without 5,000 bp 10x read coverage removed.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/patternMatcher.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Main pattern-matching function — patternMatcher","text":"","code":"patternMatcher(   VLPpileup,   WCpileup,   windowSize,   minBlockSize,   maxBlockSize,   minContigLength,   minSlope )"},{"path":"https://jlmaier12.github.io/TrIdent/reference/patternMatcher.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Main pattern-matching function — patternMatcher","text":"VLPpileup table containing contig names, coverages averaged 100 bp windows, contig positions associated mapping VLP-fraction reads whole-community contigs WCpileup table containing contig names, coverages averaged 100 bp windows, contig positions associated mapping whole-community reads whole-community contigs windowSize window size used re-average read coverage datasets minBlockSize minimum size prophage-like block pattern. Default 10,000 bp. maxBlockSize maximum size prophage-like block pattern. Default NA minContigLength minimum contig size (bp) perform pattern-matching . Must least 20,000 bp. Default 30,000 bp. minSlope minimum slope value test sloping patterns","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/patternMatcher.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Main pattern-matching function — patternMatcher","text":"List containing three objects.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/patternMatchSize.html","id":null,"dir":"Reference","previous_headings":"","what":"Pattern-match size calculator — patternMatchSize","title":"Pattern-match size calculator — patternMatchSize","text":"Calculate size (bp) matching region Prophage-like Sloping patterns","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/patternMatchSize.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pattern-match size calculator — patternMatchSize","text":"","code":"patternMatchSize(classifSumm, classifList, windowSize)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/patternMatchSize.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pattern-match size calculator — patternMatchSize","text":"classifSumm Classification summary table classifList list containing pattern match information associated contig classifications windowSize window size used re-average read coverage pileups","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/patternMatchSize.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pattern-match size calculator — patternMatchSize","text":"dataframe","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/pileupFormatter.html","id":null,"dir":"Reference","previous_headings":"","what":"Correctly formats pileup files. — pileupFormatter","title":"Correctly formats pileup files. — pileupFormatter","text":"Places columns correct order renames columns. Cleans contig labels remove excess information whitespace.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/pileupFormatter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Correctly formats pileup files. — pileupFormatter","text":"","code":"pileupFormatter(pileup)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/pileupFormatter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Correctly formats pileup files. — pileupFormatter","text":"pileup table containing contig names, read coverages averaged 100 bp windows,contig positions","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/pileupFormatter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Correctly formats pileup files. — pileupFormatter","text":"dataframe","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/plotTrIdentResults.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot read coverage graphs of contigs classified as Prophage-like, Sloping, or HighCovNoPattern — plotTrIdentResults","title":"Plot read coverage graphs of contigs classified as Prophage-like, Sloping, or HighCovNoPattern — plotTrIdentResults","text":"Plot read coverages contig associated pattern-match Prophage-like, Sloping HighCovNoPattern classifications. Returns list ggplot objects.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/plotTrIdentResults.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot read coverage graphs of contigs classified as Prophage-like, Sloping, or HighCovNoPattern — plotTrIdentResults","text":"","code":"plotTrIdentResults(   VLPpileup,   WCpileup,   TrIdentResults,   matchScoreFilter,   saveFilesTo )"},{"path":"https://jlmaier12.github.io/TrIdent/reference/plotTrIdentResults.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot read coverage graphs of contigs classified as Prophage-like, Sloping, or HighCovNoPattern — plotTrIdentResults","text":"VLPpileup VLP-fraction pileup file. WCpileup Whole-community pileup file. TrIdentResults Output `TrIdentClassifier()`. matchScoreFilter Optional, Filter plots using normalized pattern match-scores. suggested filtering threshold provided `TrIdentClassifier()` `suggFiltThresh=TRUE`. saveFilesTo Optional, Provide path directory wish save output . folder made within provided directory store results.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/plotTrIdentResults.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot read coverage graphs of contigs classified as Prophage-like, Sloping, or HighCovNoPattern — plotTrIdentResults","text":"Large list containing ggplot objects","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/plotTrIdentResults.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot read coverage graphs of contigs classified as Prophage-like, Sloping, or HighCovNoPattern — plotTrIdentResults","text":"","code":"patternMatches <- plotTrIdentResults(   VLPpileup = VLPFractionSamplePileup,   WCpileup = WholeCommunitySamplePileup,   TrIdentResults = TrIdentSampleOutput )"},{"path":"https://jlmaier12.github.io/TrIdent/reference/prophageLikeBorders.html","id":null,"dir":"Reference","previous_headings":"","what":"Prophage-like border finder — prophageLikeBorders","title":"Prophage-like border finder — prophageLikeBorders","text":"Find borders Prophage-like patterns specificity pattern-matching using 100 bp window pileups sliding standard deviation technique.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/prophageLikeBorders.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prophage-like border finder — prophageLikeBorders","text":"","code":"prophageLikeBorders(viralSubset, classificationPatterns, i, windowSize)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/prophageLikeBorders.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prophage-like border finder — prophageLikeBorders","text":"viralSubset subset read coverage pileup pertains contig currently assessed classificationPatterns pattern match information associated contig classified Prophage-like, Sloping, HighCovNoPattern index contig currently assessed windowSize window size used re-average read coverage pileups","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/prophageLikeBorders.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prophage-like border finder — prophageLikeBorders","text":"List","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/prophageLikeElevation.html","id":null,"dir":"Reference","previous_headings":"","what":"Determine Prophage-like read coverage elevation in whole-community — prophageLikeElevation","title":"Determine Prophage-like read coverage elevation in whole-community — prophageLikeElevation","text":"Determines whether detected Prophage-like genetic element read coverage whole-community either elevated depressed compared average read coverage non-prophage region.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/prophageLikeElevation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determine Prophage-like read coverage elevation in whole-community — prophageLikeElevation","text":"","code":"prophageLikeElevation(   classifSummTable,   prophageLikeClassifList,   VLPpileup,   WCpileup,   windowSize )"},{"path":"https://jlmaier12.github.io/TrIdent/reference/prophageLikeElevation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determine Prophage-like read coverage elevation in whole-community — prophageLikeElevation","text":"classifSummTable Classification summary table prophageLikeClassifList list containing pattern match information associated contigs classified Prophage-like. VLPpileup table containing contig names, coverages averaged 100 bp windows, contig positions associated mapping VLP-fraction reads whole-community contigs WCpileup table containing contig names, coverages averaged 100 bp windows, contig positions associated mapping whole-community reads whole-community contigs windowSize window size used re-average read coverage pileups","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/prophageLikeElevation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determine Prophage-like read coverage elevation in whole-community — prophageLikeElevation","text":"dataframe","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/prophageLikeZoom.html","id":null,"dir":"Reference","previous_headings":"","what":"Prophage-like pattern zoom — prophageLikeZoom","title":"Prophage-like pattern zoom — prophageLikeZoom","text":"'Zoom-' (aka subset) desired region surrounding block pattern.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/prophageLikeZoom.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prophage-like pattern zoom — prophageLikeZoom","text":"","code":"prophageLikeZoom(viralSubset, classificationPatterns, i, zoom, windowSize)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/prophageLikeZoom.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prophage-like pattern zoom — prophageLikeZoom","text":"viralSubset subset read coverage pileup pertains contig currently assessed classificationPatterns pattern match information associated contig classified Prophage-like, sloping, HighCovNoPattern index contig currently assessed zoom number rows outside start stop positions block pattern zoom-windowSize window size used re-average read coverage pileups","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/prophageLikeZoom.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prophage-like pattern zoom — prophageLikeZoom","text":"Dataframe","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/resultsHisto.html","id":null,"dir":"Reference","previous_headings":"","what":"Create histogram of normalized pattern-match scores — resultsHisto","title":"Create histogram of normalized pattern-match scores — resultsHisto","text":"Plots histogram normalized match scores Prophage-like, Sloping HighCovNoPattern classifications colors plot based classifications. suggested filtering threshold provided filtering results based quality pattern-match.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/resultsHisto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create histogram of normalized pattern-match scores — resultsHisto","text":"","code":"resultsHisto(summaryList, suggFiltThresh)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/resultsHisto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create histogram of normalized pattern-match scores — resultsHisto","text":"summaryList Classification summary table filtered include contigs Prophage-like, Sloping HighCovNoPattern classifications suggFiltThresh TRUE FALSE, Suggest filtering threshold output pattern-match score histogram. Default FALSE.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/resultsHisto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create histogram of normalized pattern-match scores — resultsHisto","text":"ggplot object","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/slopeSumm.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize slopes for sloping classifications — slopeSumm","title":"Summarize slopes for sloping classifications — slopeSumm","text":"Add slope information sloping classifications summary table","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/slopeSumm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize slopes for sloping classifications — slopeSumm","text":"","code":"slopeSumm(classifSumm, slopingClassifList, windowSize)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/slopeSumm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize slopes for sloping classifications — slopeSumm","text":"classifSumm Classification summary table slopingClassifList list containing pattern match information associated contigs classified sloping. windowSize window size used re-average read coverage pileups","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/slopeSumm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarize slopes for sloping classifications — slopeSumm","text":"dataframe","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/slopeTranslator.html","id":null,"dir":"Reference","previous_headings":"","what":"Sloping pattern translator — slopeTranslator","title":"Sloping pattern translator — slopeTranslator","text":"Translates sloping pattern containing initial jump-read coverage across contig. Translate pattern 1000 bp time. Stop translating pattern left contig reaches 20,000 bp.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/slopeTranslator.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sloping pattern translator — slopeTranslator","text":"","code":"slopeTranslator(   viralSubset,   bestMatchInfo,   windowSize,   slopeChange,   leftOrRight )"},{"path":"https://jlmaier12.github.io/TrIdent/reference/slopeTranslator.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sloping pattern translator — slopeTranslator","text":"viralSubset subset read coverage pileup pertains contig currently assessed bestMatchInfo pattern-match information associated current best pattern match. windowSize window size used re-average read coverage pileups slopeChange list containing pattern vector, slope value, value slope bottom leftOrRight direction sloping pattern. Either \"Left\" left right (neg) slopes \"Right\" right left (pos) slopes.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/slopeTranslator.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sloping pattern translator — slopeTranslator","text":"List","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/slopeWithStart.html","id":null,"dir":"Reference","previous_headings":"","what":"Sloping pattern with an initial jump-up in read coverage — slopeWithStart","title":"Sloping pattern with an initial jump-up in read coverage — slopeWithStart","text":"Build, translate, change slope sloping pattern slope start","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/slopeWithStart.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sloping pattern with an initial jump-up in read coverage — slopeWithStart","text":"","code":"slopeWithStart(viralSubset, windowSize, minSlope)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/slopeWithStart.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sloping pattern with an initial jump-up in read coverage — slopeWithStart","text":"viralSubset subset read coverage pileup pertains contig currently assessed windowSize window size used re-average read coverage pileups minSlope minimum slope value test sloping patterns","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/slopeWithStart.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sloping pattern with an initial jump-up in read coverage — slopeWithStart","text":"List containing two objects","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/specializedTransductionID.html","id":null,"dir":"Reference","previous_headings":"","what":"Identify potential specialized transduction events on contigs classified as Prophage-like — specializedTransductionID","title":"Identify potential specialized transduction events on contigs classified as Prophage-like — specializedTransductionID","text":"Search contigs classified Prophage-like dense read coverage outside pattern-match borders may indicate specialized transduction. Returns list first object containing summary table second object containing list plots associated specialzied transduction search results. plot green, identified potential specialized transduction.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/specializedTransductionID.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Identify potential specialized transduction events on contigs classified as Prophage-like — specializedTransductionID","text":"","code":"specializedTransductionID(   VLPpileup,   TrIdentResults,   specificContig,   noReadCov = 500,   specTransLength = 2000,   matchScoreFilter,   logScale = FALSE,   SaveFilesTo )"},{"path":"https://jlmaier12.github.io/TrIdent/reference/specializedTransductionID.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Identify potential specialized transduction events on contigs classified as Prophage-like — specializedTransductionID","text":"VLPpileup VLP-fraction pileup file. TrIdentResults Output `TrIdentClassifier()` specificContig Optional, Search specific contig classified Prophage-like (\"NODE_1\"). noReadCov Number basepairs zero read coverage encountered specialized transduction searching stops. Default 500. Must least 100. specTransLength Number basepairs non-zero read coverage needed specialized transduction considered. Default 2000. Must least 100. matchScoreFilter Optional, Filter plots using normalized pattern match-scores. suggested filtering threshold provided `TrIdentClassifier()` `suggFiltThresh=TRUE`. logScale TRUE FALSE, display VLP-fraction read coverage log10 scale. Default FALSE. SaveFilesTo Provide path directory wish save output . `specializedTransductionID()` make folder within provided directory store results.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/specializedTransductionID.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Identify potential specialized transduction events on contigs classified as Prophage-like — specializedTransductionID","text":"Large list containing two objects","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/specializedTransductionID.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Identify potential specialized transduction events on contigs classified as Prophage-like — specializedTransductionID","text":"","code":"specTransduction <- specializedTransductionID(   VLPpileup = VLPFractionSamplePileup,   TrIdentResults = TrIdentSampleOutput ) #> 2 contigs have potential specialized transduction #> We recommend that you also view the results of this search with #>       logScale=TRUE  specTransductionNODE62 <- specializedTransductionID(   VLPpileup = VLPFractionSamplePileup,   TrIdentResults = TrIdentSampleOutput,   specificContig = \"NODE_62\" ) #> 1 contigs have potential specialized transduction #> We recommend that you also view the results of this search with #>       logScale=TRUE"},{"path":"https://jlmaier12.github.io/TrIdent/reference/specTransductionPlot.html","id":null,"dir":"Reference","previous_headings":"","what":"Specialized transduction plot — specTransductionPlot","title":"Specialized transduction plot — specTransductionPlot","text":"Plot search results `specializedTransductionID()`","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/specTransductionPlot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Specialized transduction plot — specTransductionPlot","text":"","code":"specTransductionPlot(   viralSubsetZoom,   startPosBp,   endPosBp,   SpecTransLeft,   specTransRight,   contigName,   classifPatternMatches,   i,   specTransSumm,   logScale,   classifSumm )"},{"path":"https://jlmaier12.github.io/TrIdent/reference/specTransductionPlot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Specialized transduction plot — specTransductionPlot","text":"viralSubsetZoom contig subset surrounding Prophage-like pattern-match startPosBp Left border position endPosBp Right border position SpecTransLeft End position spec transduction left border specTransRight End position spec transduction right border contigName reference name contig currently assessed (.e \"NODE_1\") classifPatternMatches pattern match information associated contig classified prophage-like,  sloping, HighCovNoPattern index contig currently assessed specTransSumm Results spec transduction search logScale TRUE, coverage plotted log10. FALSE, raw coverage values plotted. Default FALSE. classifSumm summary information associated contig classified Prophage-like, Sloping, HighCovNoPattern","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/specTransductionPlot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Specialized transduction plot — specTransductionPlot","text":"ggplot object","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/specTransductionSearch.html","id":null,"dir":"Reference","previous_headings":"","what":"Specialized transduction search and plot — specTransductionSearch","title":"Specialized transduction search and plot — specTransductionSearch","text":"Search contigs classified prophage-like potential specialized transduction return plot visualizing search results.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/specTransductionSearch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Specialized transduction search and plot — specTransductionSearch","text":"","code":"specTransductionSearch(   contigName,   VLPpileup,   classifPatternMatches,   classifSumm,   windowSize,   i,   noReadCov,   specTransLength,   logScale )"},{"path":"https://jlmaier12.github.io/TrIdent/reference/specTransductionSearch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Specialized transduction search and plot — specTransductionSearch","text":"contigName reference name contig currently assessed (.e \"NODE_1\") VLPpileup table containing contig names, coverages averaged 100 bp windows, contig positions associated mapping VLP-fraction reads whole-community contigs classifPatternMatches pattern match information associated contig classified prophage-like,  sloping, HighCovNoPattern classifSumm summary information associated contig classified Prophage-like, Sloping, HighCovNoPattern windowSize window size used re-average read coverage pileups index contig currently assessed noReadCov many bp read coverage encountered searching stops? Default 500. specTransLength many bp read coverage look outside prophage borders? Default 2000. logScale TRUE, coverage plotted log10. FALSE, raw coverage values plotted. Default FALSE.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/specTransductionSearch.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Specialized transduction search and plot — specTransductionSearch","text":"List containing two objects","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/TrIdent-package.html","id":null,"dir":"Reference","previous_headings":"","what":"TrIdent - Transduction Identification — TrIdent-package","title":"TrIdent - Transduction Identification — TrIdent-package","text":"Automatic detection, classification characterization   transduction events transductomics datasets using read coverage   pattern-matching. Please see [Transductomics: sequencing-based detection analysis transduced DNA pure cultures microbial communities] (   https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-020-00935-5)   information transductomics method, data analysis   workflow.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/TrIdent-package.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"TrIdent - Transduction Identification — TrIdent-package","text":"three main functions TrIdent : TrIdentClassifier performs pattern-matching, classification characterization read coverage patterns contigs. plotTrIdentResults plots results  TrIdentClassifier() specializedTransductionID searches contigs classified Prophage-like TrIdentClassifier() potential specialized transduction","code":""},{"path":[]},{"path":"https://jlmaier12.github.io/TrIdent/reference/TrIdent-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"TrIdent - Transduction Identification — TrIdent-package","text":"Jessie Maier jlmaier@ncsu.edu & Jorden Rabasco   jrabasc@ncsu.edu","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/TrIdentClassifier.html","id":null,"dir":"Reference","previous_headings":"","what":"Classify contigs as Prophage-like, Sloping, HighCovNoPattern, and NoPattern — TrIdentClassifier","title":"Classify contigs as Prophage-like, Sloping, HighCovNoPattern, and NoPattern — TrIdentClassifier","text":"Performs pattern-matching summarizes results list. first item list table consisting summary information contigs passed pattern-matching (.e filtered ). second item list table consisting summary information contigs classified via pattern-matching. third item list contains pattern-match information associated contig previous table. fourth object list table containing contigs filtered prior pattern-matching. fifth item windowSize used search.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/TrIdentClassifier.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Classify contigs as Prophage-like, Sloping, HighCovNoPattern, and NoPattern — TrIdentClassifier","text":"","code":"TrIdentClassifier(   VLPpileup,   WCpileup,   windowSize = 1000,   minBlockSize = 10000,   maxBlockSize = Inf,   minContigLength = 30000,   minSlope = 0.001,   suggFiltThresh = FALSE,   SaveFilesTo )"},{"path":"https://jlmaier12.github.io/TrIdent/reference/TrIdentClassifier.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Classify contigs as Prophage-like, Sloping, HighCovNoPattern, and NoPattern — TrIdentClassifier","text":"VLPpileup VLP-fraction pileup file. WCpileup whole-community pileup file. windowSize number basepairs average read coverage values . Options 100, 200, 500, 1000 .  Default 1000. minBlockSize minimum size (bp) Prophage-like block pattern. Default 10000. Must least 1000. maxBlockSize maximum size (bp) Prophage-like block pattern. Default NA (maximum). minContigLength minimum contig size (bp) perform pattern-matching . Must least 25000. Default 30000. minSlope minimum slope value test sloping patterns. Default 0.001 (.e minimum change 10x read coverage 100,000 bp). suggFiltThresh TRUE FALSE, Suggest filtering threshold TrIdent classifications based normalized pattern-match scores. Default FALSE. SaveFilesTo Optional, Provide path directory wish save output . folder made within provided directory store results.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/TrIdentClassifier.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Classify contigs as Prophage-like, Sloping, HighCovNoPattern, and NoPattern — TrIdentClassifier","text":"Large list containing 5 objects","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/TrIdentClassifier.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Classify contigs as Prophage-like, Sloping, HighCovNoPattern, and NoPattern — TrIdentClassifier","text":"","code":"TrIdent_results <- TrIdentClassifier(   VLPpileup = VLPFractionSamplePileup,   WCpileup = WholeCommunitySamplePileup ) #> Reformatting pileup files #> Starting pattern-matching... #> A quarter of the way done with pattern-matching #> Half of the way done with pattern-matching #> Almost done with pattern-matching! #> Determining sizes (bp) of pattern matches #> Identifying highly active/abundant or heterogenously integrated #>         Prophage-like elements #> Finalizing output #> Execution time: 14.75secs #> 1 contigs were filtered out based on low read coverage #> 0 contigs were filtered out based on length #>  #> HighCovNoPattern        NoPattern    Prophage-like          Sloping  #>                1                1                4                3  #> 3 of the prophage-like classifications are highly active or abundant #> 1 of the prophage-like classifications are mixed, i.e. heterogenously #>         integrated into their bacterial host population"},{"path":"https://jlmaier12.github.io/TrIdent/reference/TrIdentSampleOutput.html","id":null,"dir":"Reference","previous_headings":"","what":"TrIdentSampleOutput — TrIdentSampleOutput","title":"TrIdentSampleOutput — TrIdentSampleOutput","text":"TrIdentClassifier output VLPFractionSamplePileup WholeCommunitySamplePileup files run default parameters Report...","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/TrIdentSampleOutput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TrIdentSampleOutput — TrIdentSampleOutput","text":"","code":"data('TrIdentSampleOutput')"},{"path":"https://jlmaier12.github.io/TrIdent/reference/TrIdentSampleOutput.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"TrIdentSampleOutput — TrIdentSampleOutput","text":"## 'TrIdentSampleOutput' list 5 objects: SummaryTable dataframe containing classifications    contigs processed pattern-matching CleanedSummaryTable SummaryTable dataframe filtered remove    contigs recieved 'None' classification PatternMatchInfo list lists containing pattern-match    information classified contig FilteredOutContigTable dataframe containing names contigs    filtered prior pattern-matching windowSize windowSize used TrIdentClassifier function (1000)","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/TrIdentSampleOutput.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"TrIdentSampleOutput — TrIdentSampleOutput","text":"list object produced TrIdentClassifier function run VLPFractionSamplePileup WholeCommunitySamplePileup files run default parameters","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/VLPFractionSamplePileup.html","id":null,"dir":"Reference","previous_headings":"","what":"VLP-Fraction of Sample Dataset — VLPFractionSamplePileup","title":"VLP-Fraction of Sample Dataset — VLPFractionSamplePileup","text":"subset contigs raw VLP-fraction read coverage pileup file generated BBMap's pileup.sh. Report...","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/VLPFractionSamplePileup.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"VLP-Fraction of Sample Dataset — VLPFractionSamplePileup","text":"","code":"data('VLPFractionSamplePileup')"},{"path":"https://jlmaier12.github.io/TrIdent/reference/VLPFractionSamplePileup.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"VLP-Fraction of Sample Dataset — VLPFractionSamplePileup","text":"## 'VLPFractionSamplePileup' data frame 10,805 rows 4   columns: V1 Contig accession V2 Mapped read coverage averaged 100 bp window size V3 Starting position (bp) 100 bp window. Restarts 0  start new contig. V4 Starting position (bp) 100 bp window. restart  start new contig.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/VLPFractionSamplePileup.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"VLP-Fraction of Sample Dataset — VLPFractionSamplePileup","text":"<https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-020-00935-5>","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/VLPFractionSamplePileup.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"VLP-Fraction of Sample Dataset — VLPFractionSamplePileup","text":"dataset represents one half complete transductomics dataset comprised two parts-whole-community fraction viral-like particle (VLP)-fraction. dataset represents VLP fraction generated purifying VLPs conventional mouse fecal homogenate using CsCl density gradient ultracentrifugation. VLP-fraction extracted DNA sequenced Illumina (paired-end mode, 150 bp reads) sequencing reads mapped associated whole-community assembly using BBMap. bbmap.sh bincov parameter covbinsize=100 used create pileup file 100 bp windows. subset 10 contigs pileup file selected sample dataset. contigs chosen associated read coverage patterns VLP-fraction exemplify TrIdent's pattern-matching functionality across classifications: NODE_617:Prophage-like, active/abundant, spec transduction NODE_135:Prophage-like, one side contig, spec transduction NODE_352:Sloping, left right slope NODE_251: Sloping, right left slope NODE_2060: Sloping, right left slope start NODE_1401: None, pattern match NODE_62: Prophage-like, spec transduction NODE_368: Prophage-like, homogeneously integrated/present, spec transduction NODE_560: HighCovNoPattern NODE_1165: None, filtered access sequencing data used generate pileup file additional details assembly mapping parameters, refer reference : Reference: Kleiner, M., Bushnell, B., Sanderson, K.E. et al. Transductomics: sequencing-based detection analysis transduced DNA pure cultures microbial communities. Microbiome 8, 158 (2020). https://doi.org/10.1186/s40168-020-00935-5","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/VLPtoWCRatioCalc.html","id":null,"dir":"Reference","previous_headings":"","what":"VLP-fraction:whole-community read coverage ratio calculator — VLPtoWCRatioCalc","title":"VLP-fraction:whole-community read coverage ratio calculator — VLPtoWCRatioCalc","text":"Calculate VLP-fraction:whole-community read coverage ratio every contig using median read coverage values. ratio greater 2 (.e VLP-fraction read coverage , average, least double whole-community read coverage), contig classified HighCovNoPattern","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/VLPtoWCRatioCalc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"VLP-fraction:whole-community read coverage ratio calculator — VLPtoWCRatioCalc","text":"","code":"VLPtoWCRatioCalc(classifSumm, WCpileup, VLPpileup)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/VLPtoWCRatioCalc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"VLP-fraction:whole-community read coverage ratio calculator — VLPtoWCRatioCalc","text":"classifSumm Classification summary table WCpileup table containing contig names, coverages averaged 100 bp windows, contig positions associated mapping whole-community reads whole-community contigs VLPpileup table containing contig names, coverages averaged 100 bp windows, contig positions associated mapping VLP-fraction reads whole-community contigs","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/VLPtoWCRatioCalc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"VLP-fraction:whole-community read coverage ratio calculator — VLPtoWCRatioCalc","text":"dataframe","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/WholeCommunitySamplePileup.html","id":null,"dir":"Reference","previous_headings":"","what":"Whole-Community Fraction of Sample Dataset — WholeCommunitySamplePileup","title":"Whole-Community Fraction of Sample Dataset — WholeCommunitySamplePileup","text":"subset contigs raw whole-community fraction read coverage pileup file generated read mapping. Report...","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/WholeCommunitySamplePileup.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Whole-Community Fraction of Sample Dataset — WholeCommunitySamplePileup","text":"","code":"data('WholeCommunitySamplePileup')"},{"path":"https://jlmaier12.github.io/TrIdent/reference/WholeCommunitySamplePileup.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Whole-Community Fraction of Sample Dataset — WholeCommunitySamplePileup","text":"## 'WholeCommunitySamplePileup' data frame 10,805 rows 4   columns: V1 Contig accession V2 Mapped read coverage averaged 100 bp window size V3 Starting position (bp) 100 bp window. Restarts 0  start new contig. V4 Starting position (bp) 100 bp window. restart  start new contig.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/WholeCommunitySamplePileup.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Whole-Community Fraction of Sample Dataset — WholeCommunitySamplePileup","text":"<https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-020-00935-5>","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/WholeCommunitySamplePileup.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Whole-Community Fraction of Sample Dataset — WholeCommunitySamplePileup","text":"dataset represents one half complete transductomics dataset comprised two parts-whole-community fraction viral-like particle (VLP)-fraction. dataset represents whole-community fraction generated conventional mouse fecal homogenate. whole-community extracted DNA sequenced Illumina (paired-end mode, 150 bp reads) metagenome assembled. sequencing reads mapped assembled contigs using BBMap. bbmap.sh bincov parameter covbinsize=100 used create pileup file 100 bp windows. subset 10 contigs pileup file selected sample dataset. contigs chosen associated read coverage patterns VLP-fraction exemplify TrIdent's pattern-matching characterization functionality across classifications: NODE_617:Prophage-like, active/abundant, spec transduction NODE_135:Prophage-like, one side contig, spec transduction NODE_352:Sloping, left right slope NODE_251: Sloping, right left slope NODE_2060: Sloping, right left slope start NODE_1401: None, pattern match NODE_62: Prophage-like, spec transduction NODE_368: Prophage-like, homogeneously integrated/present, spec transduction NODE_560: HighCovNoPattern NODE_1165: None, filtered access sequencing data used generate pileup file additional details assembly mapping parameters, refer reference : Reference: Kleiner, M., Bushnell, B., Sanderson, K.E. et al. Transductomics: sequencing-based detection analysis transduced DNA pure cultures microbial communities. Microbiome 8, 158 (2020). https://doi.org/10.1186/s40168-020-00935-5","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/zeroCountSearch.html","id":null,"dir":"Reference","previous_headings":"","what":"Counts zero values to the left and right of prophage-like borders — zeroCountSearch","title":"Counts zero values to the left and right of prophage-like borders — zeroCountSearch","text":"Checks see point number consecutive zero values left right prophage-like pattern match borders equals noReadCov parameter","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/zeroCountSearch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Counts zero values to the left and right of prophage-like borders — zeroCountSearch","text":"","code":"zeroCountSearch(startOrEnd, viralSubsetZoom, startOrEndPosRow, noReadCov)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/zeroCountSearch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Counts zero values to the left and right of prophage-like borders — zeroCountSearch","text":"startOrEnd searching start (left side) end (right side) prophage-like pattern-match viralSubsetZoom viralSubset dataframe subsetted 50,000 bp outside pattern match borders startOrEndPosRow row index start end position prophage-like pattern match noReadCov many bp read coverage encountered specialized transduction searching stops? Default 500.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/zeroCountSearch.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Counts zero values to the left and right of prophage-like borders — zeroCountSearch","text":"List","code":""},{"path":"https://jlmaier12.github.io/TrIdent/news/index.html","id":"trident-0990","dir":"Changelog","previous_headings":"","what":"TrIdent 0.99.0","title":"TrIdent 0.99.0","text":"Initial CRAN submission.","code":""}]
+[{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"TrIdent","text":"TrIdent- Transduction Identification TrIdent consists three main functions run following order: TrIdentClassifier(): Classifies contigs ‘Prophage-like’, ‘Sloping’, ‘HighCovNoPattern’, ‘NoPattern’ using read coverage pattern-matching. plotTrIdentResults(): Plots pattern-matching results TrIdentClassifier(). specializedTransductionID(): Searches contigs classified Prophage-like TrIdentClassifier() associated specialized transduction events. TrIdent automates analysis transductomics data detecting, classifying, characterizing read coverage patterns associated potential transduction events. Transductomics, developed Kleiner et al.  (2020), DNA sequencing-based method detection characterization transduction events pure cultures complex communities. Transductomics relies mapping sequencing reads viral-like particle (VLP)-fraction sample contigs assembled metagenome (whole-community) sample. Reads bacterial DNA carried VLPs map back bacterial contigs origin creating read coverage patterns indicative ongoing transduction. read coverage patterns detected represent DNA actively carried transduced VLPs. read coverage patterns represent complete transduction events (.e integration transduced DNA new bacterial chromosomes). Reference: Kleiner, M., Bushnell, B., Sanderson, K.E. et al.  Transductomics: sequencing-based detection analysis transduced DNA pure cultures microbial communities. Microbiome 8, 158 (2020). https://doi.org/10.1186/s40168-020-00935-5","code":""},{"path":[]},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"bioconductor-install","dir":"Articles","previous_headings":"Introduction","what":"Bioconductor install","title":"TrIdent","text":"","code":"if (!require(\"BiocManager\", quietly = TRUE)) {   install.packages(\"BiocManager\") }  BiocManager::install(\"TrIdent\") library(TrIdent)"},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"github-install","dir":"Articles","previous_headings":"Introduction","what":"GitHub install","title":"TrIdent","text":"","code":"BiocManager::install(\"jlmaier12/TrIdent\") library(TrIdent)"},{"path":[]},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"transductomics-data","dir":"Articles","previous_headings":"Input Data","what":"Transductomics data","title":"TrIdent","text":"Transductomics allows identification bacterial DNA actively carried transduced VLPs. transductomics dataset consists two parts- metagenomes whole-community VLP fractions sample. whole-community fraction generated extracting sequencing DNA whole sample. VLP-fraction generated extraction sequencing DNA ultra-purified VLPs sample. VLP ultra-purification generally done using CsCl density-gradient ultracentrifugation. Additionally, important VLP-fraction treated DNase remove free DNA! sequencing, reads whole-community fraction assembled whole-community VLP-fraction reads mapped assembly. Read mapping performed using high minimum identity (0.97 higher) random mapping ambiguous reads. pileup files needed TrIdent generated using .bam files produced read mapping. Deep sequencing whole-community VLP-fractions needed transductomics! Sample preparation, sequencing procedures, bioinformatics methods detailed Kleiner et al.(2020).","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"pileup-files","dir":"Articles","previous_headings":"Input Data","what":"Pileup files","title":"TrIdent","text":"TrIdent detects read coverage patterns using pattern-matching algorithm operates pileup files. pileup file file format row summarizes ‘pileup’ reads specific genomic locations. Pileup files can used generate rolling mean read coverages associated base pair positions across metagenome assembly reduces data size preserving read coverage patterns. TrIdent requires input pileups files generated using 100 bp window/bin size. read mappers, like BBMap, allow generation pileup files bbmap.sh command use bincov output covbinsize=100 parameter/argument. Otherwise, BBMap’s pileup.sh can convert .bam files produced read mapper pileup files compatible TrIdent using bincov output binsize=100. TrIdent requires two pileup files transductomics dataset input: VLP-fraction pileup: Sequencing reads sample’s ultra-purified VLP-fraction mapped sample’s whole-community metagenome assembly. whole-community pileup: Sequencing reads sample’s whole-community mapped sample’s whole-community metagenome assembly. Remember- data used pileup file must originate sample. Pileup files must use 100 bp window/bin size rolling mean. input pileup files must following format: Dataframe four columns: V1: Contig accession V2: Mapped read coverage values averaged 100 bp windows V3: Starting position (bp) 100 bp window. Restarts 0 start new contig. V4: Starting position (bp) 100 bp window. restart start new contig.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"tridentclassifier","dir":"Articles","previous_headings":"","what":"TrIdentClassifier()","title":"TrIdent","text":"TrIdentClassifier() main function TrIdent. function filters contigs based length read coverage, performs pattern-matching classify contigs, identifies highly active/abundant heterogenously integrated Prophage-like elements, determines contigs high VLP-fraction:whole-community read coverage ratios, identifies start stop positions sizes pattern-matches, calculates slopes Sloping pattern-matches. Note TrIdentClassifier() results taken face value manual curation needed! recommend careful examination output plots determine agree TrIdentClassifier() classifications.","code":""},{"path":[]},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"contig-filtering","dir":"Articles","previous_headings":"TrIdentClassifier() > Function components","what":"Contig filtering","title":"TrIdent","text":"Contigs short little read coverage filtered prior pattern-matching. TrIdentClassifier() filters contigs least 10x coverage total 5,000 bp across whole contig. read coverage filtering done way avoid filtering long contigs short Prophage-like patterns might get removed filtering done read coverage averages medians. Additionally, contigs less 30,000 bp filtered default, however can changed minContigLength parameter. contigs shorter 30,000 bp may poor quality often long enough capture complete transduction patterns, allow users set minimum minContigLength 25,000 bp. like reduce size input pileup files TrIdent, consider pre-filtering assembly contigs greater 25,000 bp prior read mapping! expected majority contigs dataset filtered due low read coverage step! contigs filtered due low read coverage, may indication DNA contamination VLP-fraction.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"changing-pileup-windowsize","dir":"Articles","previous_headings":"TrIdentClassifier() > Function components","what":"Changing pileup windowSize","title":"TrIdent","text":"input pileup files 100 bp windows mapped read coverage averaged . small window size needed detect read coverage patterns associated specialized transduction may span thousand basepairs. However, read coverage patterns associated types transduction generally don’t require resolution 100 bp windows provide. users can use 100 bp windowSize TrIdentClassifier(), processing time increased significantly noisy data may interfere pattern-matching. find default 1,000 bp windowSize provides nice balance processing time read coverage pattern resolution.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"pattern-matching","dir":"Articles","previous_headings":"TrIdentClassifier() > Function components","what":"Pattern-matching","title":"TrIdent","text":"TrIdentClassifier() detects read coverage patterns VLP-fraction using pattern-matching approach. Several predefined patterns, described , built using specific length read coverage values contig assessed. Patterns translated across contig 1,000 bp sliding windows translation, pattern-match score calculated taking mean absolute difference VLP-fraction read coverage pattern values. smaller match-score, better pattern-match. pattern fully translated across contig, certain aspects pattern changed (.e. height, width, slope) translation repeated. process translation pattern re-scaling repeated large number pattern variations tested. pattern-matching complete, pattern associated best match-score used contig classification. Contigs classified ‘Prophage-like’, ‘Sloping’, ‘NoPattern’ pattern-matching.","code":""},{"path":[]},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"sloping","dir":"Articles","previous_headings":"","what":"TrIdent","title":"TrIdent","text":"four sloping pattern variations sloping pattern class. sloping patterns representative large DNA transfers take place generalized, lateral gene transfer agent (GTA) transduction due decreasing frequency DNA packaging moving away packaging initiation sites. pattern-matching, slope values sloping patterns decreased minimum slope 0.001 (change 10x read coverage 10,000 bp) reached. minimum slope value can changed minSlope parameter. Generalized, lateral GTA transduction events can span tens hundreds kilobasepairs DNA single contig typically capture entire event. Depending part transducing event captured contig, sloping can severe almost 0. Patterns 1 2 represent contigs capture Sloping transducing event somewhere middle DNA transfer. Patterns 2 4 represent contigs capture jump read coverage associated packaging initiation site Sloping transducing event. Patterns 2 4 translated across contig addition slopes changed slopes changed patterns 1 2.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"prophage-like","dir":"Articles","previous_headings":"","what":"TrIdent","title":"TrIdent","text":"three block patterns Prophage-like pattern class. block patterns representative integrated genetic elements can excised host chromosome mobilized. blocks read coverage define classification formed reads mobilized genetic elements packaged VLPs map back respective integration sites host bacterium’s chromosome. Prophage, phage-inducible chromosomal islands (PICIs), transposons examples genetic elements fall Prophage-like class. pattern-matching, heights widths block patterns altered pattern variations translated across contig. block pattern widths never get smaller 10,000 bp default, however can changed minBlockSize parameter. Pattern 1 represents Prophage-like element entirely contig patterns 2 3 represent Prophage-like elements trail right left side contig, respectively. Prophage-like classification example transduction , may transduction associated Prophage-like classifications. improper excision Prophage-like elements may lead specialized transduction genes neighboring element’s integration site. TrIdent’s specializedTransductionID() function (explained detail ) attempt detect specialized transduction events associated Prophage-like classifications.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"nopattern","dir":"Articles","previous_headings":"","what":"TrIdent","title":"TrIdent","text":"Since best pattern-match contig determined comparing match-scores amongst pattern-variations pattern classes, needed ‘negative control’ pattern compare . ‘NoPattern’ ‘pattern’ serves negative control matching contigs read coverage patterns. made two NoPattern patterns consist horizontal line length contig assessed either average median read coverage contig. pattern re-scaled translated way. Note read coverage patterns heavily dependent depth read coverage achieved sequencing therefore rare transduction events may achieve sufficient read coverage detection read coverage pattern-matching. Rather label contigs read coverage pattern ‘transduction’, instead label ‘pattern’.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"highly-activeabundant-and-heterogenously-integratedpresent-prophage-like-elements","dir":"Articles","previous_headings":"TrIdentClassifier() > Function components","what":"Highly active/abundant and heterogenously integrated/present Prophage-like elements","title":"TrIdent","text":"Prophage-like elements actively replicating highly abundant typically generate sequencing reads rest host bacterium’s chromosome. may create region elevated read coverage element’s insertion site whole-community fraction read coverage. Conversely, Prophage-like element integrated portion host bacterial population, may dip depression read coverage integration site whole-community read coverage. order determine whole-community read coverage elevated depressed site Prophage-like element, one must know Prophage-like element’s genomic location. tools rely annotation information identify Prophage-like elements whole-community metagenomes, TrIdentClassifier() uses VLP-fraction read coverage patterns. locations Prophage-like pattern-matches used calculate Prophage-like:non-Prophage-like whole-community read coverage ratio. Prophage-like patterns whole-community read coverage ratios greater 1.15 labeled ‘elevated’ ratios less 0.75 labeled ‘depressed’.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"nopattern-classifications-with-high-vlp-fractionwhole-community-read-coverage-ratios","dir":"Articles","previous_headings":"TrIdentClassifier() > Function components","what":"NoPattern classifications with high VLP-fraction:whole-community read coverage ratios","title":"TrIdent","text":"contig receives noPattern classification, proceeds additional classification step either leaves classification re-classifies contig high VLP-fraction:whole-community read coverage ratio (‘HighCovNoPattern’). words, contigs HighCovNoPattern classification even read coverage across contig (.e. notable read coverage pattern) VLP-fraction read coverage notably higher whole-community read coverage. re-classification necessary certain biologically significant events may interest user can characteristics. First, certain transduction events, specifically associated Sloping classification, may long extend across multiple contigs. ‘tails’ sloping patterns created events may little actual sloping (pattern) relatively high read coverage (Fig S2 Kleiner et al., 2020). Second, evidence membrane vesicle (MV) mediated transduction (also known vesiduction protected extracellular transformation) produces relatively even read coverage patterns purified MV sequencing reads mapped back bacterial chromosome origin (Faddetta et al., 2022). Lastly, phage genomes assembled contigs whole-community fraction may generate high levels even read coverage phage reads VLP-fraction map back genome sequences. Contigs median VLP-fraction:Whole-community read coverage ratios greater 2, words contigs median VLP-fraction read coverage value 2x whole-community median read coverage value, re-classified HighCovNoPattern. Reference: Faddetta, T., Vassallo, ., Del Duca, S. et al. Unravelling DNA sequences carried Streptomyces coelicolor membrane vesicles. Sci Rep 12, 16651 (2022). https://doi.org/10.1038/s41598-022-21002-z","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"usage","dir":"Articles","previous_headings":"TrIdentClassifier()","what":"Usage","title":"TrIdent","text":"Default arguments:","code":"TrIdentOutput <- TrIdentClassifier(   VLPpileup = VLPFractionSamplePileup,   WCpileup = WholeCommunitySamplePileup ) #> Reformatting pileup files #> Starting pattern-matching... #> A quarter of the way done with pattern-matching #> Half of the way done with pattern-matching #> Almost done with pattern-matching! #> Determining sizes (bp) of pattern matches #> Identifying highly active/abundant or heterogenously integrated #>       Prophage-like elements #> Finalizing output #> Execution time: 24.25secs #> 1 contigs were filtered out based on low read coverage #> 0 contigs were filtered out based on length #>  #> HighCovNoPattern        NoPattern    Prophage-like          Sloping  #>                1                1                4                3 #> 3 of the prophage-like classifications are highly active or abundant #> 1 of the prophage-like classifications are mixed, i.e. heterogenously #>         integrated into their bacterial host population"},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"argumentsparameters","dir":"Articles","previous_headings":"TrIdentClassifier()","what":"Arguments/Parameters","title":"TrIdent","text":"VLPpileup: VLP-fraction pileup file. WCpileup: Whole-community pileup file. windowSize: number basepairs average read coverage values . Options 100, 200, 500, 1000 . Default 1000. minBlockSize: minimum size (bp) Prophage-like block pattern. Default 10000. Must greater 1000. maxBlockSize: maximum size (bp) Prophage-like block pattern. Default NA (maximum). minContigLength: minimum contig size (bp) perform pattern-matching . Must least 25000. Default 30000. minSlope: minimum slope value test sloping patterns. Default 0.001 (.e minimum change 10x read coverage 100,000 bp). suggFiltThresh: TRUE FALSE, Suggest filtering threshold TrIdent classifications based normalized pattern-match scores. Default FALSE. verbose: TRUE FALSE. Print progress messages console. Default TRUE. SaveFilesTo: Optional, Provide path directory wish save output . folder made within provided directory store results.","code":"TrIdentClassifier(VLPpileup, WCpileup,   windowSize = 1000, minBlockSize = 10000,   maxBlockSize = Inf, minContigLength = 30000, minSlope = 0.001,   suggFiltThresh = FALSE, verbose = TRUE, SaveFilesTo )"},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"output","dir":"Articles","previous_headings":"TrIdentClassifier()","what":"Output","title":"TrIdent","text":"output TrIdentClassifier() list containing five objects: SummaryTable: table containing classification information contigs filtered . CleanedSummaryTable: cleaned summary table containing classification information contigs classified Prophage-like, Sloping HighCovNoPattern. PatternMatchInfo: list pattern-match information used functions TrIdent. FilteredOutContigTable: table containing contigs filtered reason (low read coverage short). windowSize: windowSize used. ResultHistogram: histogram displaying overall abundance quality pattern-matches addition composition classifications. displayed pattern-match scores normalized dividing score associated contig length. scores normalized visualize overall quality pattern-matching entire dataset. Remember, smaller pattern-match scores correspond better pattern-matches. Save desired list-item new variable using associated name. Summary table:","code":"TrIdentSummaryTable <- TrIdentOutput$SummaryTable"},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"plottridentresults","dir":"Articles","previous_headings":"","what":"plotTrIdentResults()","title":"TrIdent","text":"plotTrIdentResults() allows users visualize whole-community VLP-fraction read coverage pattern-match associated contig classified Prophage-like, Sloping HighCovNoPattern.","code":""},{"path":[]},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"re-building-pattern-matches","dir":"Articles","previous_headings":"plotTrIdentResults() > Function components","what":"Re-building pattern-matches","title":"TrIdent","text":"TrIdentClassifier() output contains information needed re-build pattern-match used contig classification. re-build complete pattern-match visualization, plotTrIdentResults() uses pattern-match’s minimum maximum values start stop positions.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"plotting-read-coverage-and-associated-pattern-matches","dir":"Articles","previous_headings":"plotTrIdentResults() > Function components","what":"Plotting read coverage and associated pattern-matches","title":"TrIdent","text":"whole-community VLP-fraction read coverage plotted contig classified Prophage-like, Sloping HighCovNoPattern. pattern-match associated classification overlaid VLP-fraction read coverage. whole-community read coverage displayed visualization elevated depressed Prophage-like region read coverage.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"usage-1","dir":"Articles","previous_headings":"plotTrIdentResults()","what":"Usage","title":"TrIdent","text":"Default arguments:","code":"TrIdentPlots <- plotTrIdentResults(   VLPpileup = VLPFractionSamplePileup,   WCpileup = WholeCommunitySamplePileup,   TrIdentResults = TrIdentOutput )"},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"argumentsparameters-1","dir":"Articles","previous_headings":"plotTrIdentResults()","what":"Arguments/Parameters","title":"TrIdent","text":"VLPpileup: VLP-fraction pileup file. WCpileup: Whole-community pileup file. TrIdentResults: output TrIdentClassifier() matchScoreFilter: Optional, Filter plots using normalized pattern match-scores. suggested filtering threshold provided TrIdentClassifier() suggFiltThresh=TRUE. saveFilesTo: Optional, Provide path directory wish save output . folder made within provided directory store results.","code":"plotTrIdentResults(   VLPpileup, WCpileup, TrIdentResults, matchScoreFilter,   saveFilesTo )"},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"output-1","dir":"Articles","previous_headings":"plotTrIdentResults()","what":"Output","title":"TrIdent","text":"output plotTrIdentResults() list containing ggplot objects. list contains read coverage plots contigs classified Sloping, Prophage-like, HighCovNoPattern respective pattern-matches. default, plots displayed raw read coverage values. recommend users also view plots using logScale=TRUE specialized transduction patterns occur low frequencies can visualized using log scaled read coverage values. View plots:  View one plot:","code":"TrIdentPlots TrIdentPlots$NODE_62"},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"specializedtransductionid","dir":"Articles","previous_headings":"","what":"specializedTransductionID()","title":"TrIdent","text":"Specialized transduction occurs integrated Prophage-like element excises packages small portion bacterial DNA directly outside borders insertion site. specializedTransductionID() searches contigs classified Prophage-like dense read coverage outside borders Prophage-like patterns might represent specialized transduction events. specialized transduction tends fairly short (couple kbps) compared generalized, lateral GTA transduction (tens hundreds kbps), averaging read coverage 1,000 bp distance (.e using windowSize=1000) can ‘blur’ specialized transduction patterns. specialized transduction identified TrIdentClassifier(). Instead, use locations Prophage-like elements identified TrIdentClassifier() guide search specialized transduction specializedTransductionID(). Note specializedTransductionID() results taken face value manual curation needed! recommend careful examination output plots determine agree specializedTransductionID() results. Setting logScale=TRUE plot read coverage log10 scale may help visualization low-frequency specialized transduction events. aware cases, log scaled read coverage can obfuscate Prophage-like element pattern .","code":""},{"path":[]},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"zoom-in-on-prophage-like-elements","dir":"Articles","previous_headings":"specializedTransductionID() > Function components","what":"Zoom-in on Prophage-like elements","title":"TrIdent","text":"Since, specialized transduction read coverage patterns relatively small, specializedTransductionID() ‘zooms-’ Prophage-like elements aid specialized transduction visualization. ‘zoom-’ Prophage-like elements, specializedTransductionID() uses pattern-match information generated TrIdentClassifier() subset contig 50,000 bp outside pattern-match borders.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"identify-borders-of-prophage-like-elements","dir":"Articles","previous_headings":"specializedTransductionID() > Function components","what":"Identify borders of Prophage-like elements","title":"TrIdent","text":"Since windowSize used pattern-matching TrIdentClassifier() likely larger 100 bp, Prophage-like pattern-match border locations directly translate border locations 100 bp windowSize. re-identify borders Prophage-like elements, use rolling standard deviation (SD) detect large changes read coverage associated Prophage-like element borders. First, contig subset surrounding left right pattern-match borders. contigs Prophage-like pattern-match trails side contig, border falls contig subset. Next, subset, rolling SD calculated read coverage value contig position associated largest SD chosen border location. border locations marked output plots black vertical lines.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"search-for-specialized-transduction-outside-prophage-like-borders","dir":"Articles","previous_headings":"specializedTransductionID() > Function components","what":"Search for specialized transduction outside Prophage-like borders","title":"TrIdent","text":"Prophage-like element borders identified, specializedTransductionID() starts border locations searches outwards dense read coverage meet ‘requirements’ specialized transduction defined two parameters specializedTransductionID(): noReadCov specTransLength specializedTransductionID() first makes sure coverage detects outside borders disrupted defined region read coverage (noReadCov). default value noReadCov 500 bp. Secondly, specializedTransductionID ensures read coverage detects outside Prophage-like borders meets minimum length requirement (specTransLength). default value specTransLength 2000 bp. default, specializedTransductionID() search coverage directly outside Prophage-like borders least 2000 bp long interrupted point 500 bp read coverage. requirements met, specializedTransductionID() label contig specialized transduction. ‘end’ specialized transduction region marked output plots red vertical lines. Additionally, read coverage plots contigs specialized transduction colored green instead blue.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"usage-2","dir":"Articles","previous_headings":"specializedTransductionID()","what":"Usage","title":"TrIdent","text":"Default arguments:","code":"SpecTransduc <- specializedTransductionID(   VLPpileup = VLPFractionSamplePileup,   TrIdentResults = TrIdentOutput ) #> 2 contigs have potential specialized transduction #> We recommend that you also view the results of this search with #>       logScale=TRUE"},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"argumentsparameters-2","dir":"Articles","previous_headings":"specializedTransductionID()","what":"Arguments/Parameters","title":"TrIdent","text":"VLPpileup: VLP-fraction pileup file. TrIdentResults: output TrIdentClassifier(). noReadCov: Number basepairs zero read coverage encountered specialized transduction searching stops. Default 500. Must least 100. specTransLength: Number basepairs non-zero read coverage needed specialized transduction considered. Default 2000. Must least 100. logScale: TRUE FALSE, display VLP-fraction read coverage log10 scale. Default FALSE. matchScoreFilter: Optional, Filter plots using normalized pattern match-scores. suggested filtering threshold provided TrIdentClassifier() suggFiltThresh=TRUE. verbose: TRUE FALSE. Print progress messages console. Default TRUE. SaveFilesTo: Optional, Provide path directory wish save output . folder made within provided directory store results. specificContig: Optional, Search specific contig classified Prophage-like (“NODE_1”).","code":"specializedTransductionID(VLPpileup, TrIdentResults,   noReadCov = 500, specTransLength = 2000,   logScale = FALSE, verbose = TRUE, matchScoreFilter,   SaveFilesTo, specificContig )"},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"output-2","dir":"Articles","previous_headings":"specializedTransductionID()","what":"Output","title":"TrIdent","text":"output specializedTransductionID() list containing two objects: summaryTable: table containing specializedTransductionID() results contigs classified Prophage-like TrIdentClassifier(). Plots: list ggplot objects contigs classified Prophage-like. plots ‘zoomed-’ Prophage-like pattern aid specialized transduction visualization. Prophage-like element borders identified specializedTransductionID() marked plot black vertical lines. specializedTransductionID() identifies potential specialized transduction, plot colored green instead blue. end specialized transduction marked red vertical line. Save desired list-item new variable using associated name. Summary table: View plots:  View specific plot:","code":"SpecializedTransducSummaryTable <- SpecTransduc$summaryTable SpecTransduc$Plots SpecTransduc$Plots$NODE_62"},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"generate-final-trident-summary-table","dir":"Articles","previous_headings":"","what":"Generate final TrIdent summary table","title":"TrIdent","text":"’d like combine summary tables produced TrIdentClassifier() specializedTransductionID(), try following:","code":"FinalTrIdentSummaryTable <- merge(TrIdentSummaryTable,   SpecializedTransducSummaryTable,   by = \"contigName\", all.x = TRUE )"},{"path":[]},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"acknowledgments","dir":"Articles","previous_headings":"Supplemental information","what":"Acknowledgments","title":"TrIdent","text":"TrIdent result combined effort brain power many individuals. Specifically, like thank Dr. Manuel Kleiner, Dr. Ben Callahan, Dr. Breck Duerkop Dr. Craig Gin individual expertise overall support!","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"funding","dir":"Articles","previous_headings":"Supplemental information","what":"Funding","title":"TrIdent","text":"development TrIdent supported seed grant North Carolina State University Data Science Academy National Institutes Health Award Numbers R35GM138362 R01Al171046.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/articles/TrIdent-vignette.html","id":"session-information","dir":"Articles","previous_headings":"Supplemental information","what":"Session Information","title":"TrIdent","text":"","code":"sessionInfo() #> R version 4.2.1 (2022-06-23 ucrt) #> Platform: x86_64-w64-mingw32/x64 (64-bit) #> Running under: Windows 10 x64 (build 19045) #>  #> Matrix products: default #>  #> locale: #> [1] LC_COLLATE=English_United States.utf8  #> [2] LC_CTYPE=English_United States.utf8    #> [3] LC_MONETARY=English_United States.utf8 #> [4] LC_NUMERIC=C                           #> [5] LC_TIME=English_United States.utf8     #>  #> attached base packages: #> [1] stats     graphics  grDevices utils     datasets  methods   base      #>  #> other attached packages: #> [1] kableExtra_1.4.0 ggplot2_3.5.1    patchwork_1.3.0  knitr_1.49       #> [5] TrIdent_0.99.2   BiocStyle_2.26.0 #>  #> loaded via a namespace (and not attached): #>  [1] tidyselect_1.2.1    xfun_0.49           bslib_0.8.0         #>  [4] purrr_1.0.2         colorspace_2.1-1    vctrs_0.6.5         #>  [7] generics_0.1.3      htmltools_0.5.8.1   viridisLite_0.4.2   #> [10] yaml_2.3.10         utf8_1.2.4          rlang_1.1.4         #> [13] pkgdown_2.1.1       jquerylib_0.1.4     pillar_1.9.0        #> [16] glue_1.8.0          withr_3.0.2         lifecycle_1.0.4     #> [19] stringr_1.5.1       munsell_0.5.1       gtable_0.3.6        #> [22] ragg_1.3.3          htmlwidgets_1.6.4   evaluate_1.0.1      #> [25] labeling_0.4.3      fastmap_1.2.0       fansi_1.0.6         #> [28] Rcpp_1.0.13-1       scales_1.3.0        BiocManager_1.30.25 #> [31] cachem_1.1.0        desc_1.4.3          RcppParallel_5.1.9  #> [34] jsonlite_1.8.9      farver_2.1.2        systemfonts_1.1.0   #> [37] fs_1.6.5            textshaping_0.4.1   digest_0.6.37       #> [40] stringi_1.8.4       bookdown_0.41       dplyr_1.1.4         #> [43] roll_1.1.7          grid_4.2.1          cli_3.6.2           #> [46] tools_4.2.1         magrittr_2.0.3      sass_0.4.9          #> [49] tibble_3.2.1        tidyr_1.3.1         pkgconfig_2.0.3     #> [52] xml2_1.3.6          rmarkdown_2.29      svglite_2.1.3       #> [55] rstudioapi_0.17.1   R6_2.5.1            compiler_4.2.1"},{"path":"https://jlmaier12.github.io/TrIdent/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Jessie Maier. Author, maintainer. Jorden Rabasco. Author, contributor. Craig Gin. Author. Benjamin Callahan. Author. Manuel Kleiner. Author, thesis advisor.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Maier J, Rabasco J, Gin C, Callahan B, Kleiner M (2025). TrIdent: TrIdent - Transduction Identification. https://github.com/jlmaier12/TrIdent, https://jlmaier12.github.io/TrIdent/.","code":"@Manual{,   title = {TrIdent: TrIdent - Transduction Identification},   author = {Jessie Maier and Jorden Rabasco and Craig Gin and Benjamin Callahan and Manuel Kleiner},   year = {2025},   note = {https://github.com/jlmaier12/TrIdent, https://jlmaier12.github.io/TrIdent/}, }"},{"path":"https://jlmaier12.github.io/TrIdent/index.html","id":"trident","dir":"","previous_headings":"","what":"TrIdent - Transduction Identification","title":"TrIdent - Transduction Identification","text":"TrIdent - Transduction Identification TrIdent automates analysis transductomics data detecting, classifying, characterizing read coverage patterns associated potential transduction events. Transductomics, developed Kleiner et al. (2020), DNA sequencing-based method detection characterization transduction events pure cultures complex communities. Transductomics relies mapping sequencing reads viral-like particle (VLP)-fraction sample contigs assembled metagenome (whole-community) sample. Reads bacterial DNA carried VLPs map back bacterial contigs origin creating read coverage patterns indicative ongoing transduction. read coverage patterns detected represent DNA actively carried transduced VLPs. read coverage patterns represent complete transduction events (.e integration transduced DNA new bacterial chromosomes). obtain data needed transductomics, microbiome sample interest split prepare two sub-sample types: - Whole-community: Represents ‘whole-community’ (bacteria, fungi, virus, etc) microbiome interest - VLP-fraction: Represents virus ‘viral-like particles’ associated microbiome interest - VLP-fraction must obtained appropriate ultra-purification protocol sample type remove bacterial cells contaminating free bacterial DNA. transductomics TrIdent, researcher can obtain information phage-host pairs involved transduction, types transduction occuring, region host genome potentially transduced, allows exploration transferred genes. Reference: Kleiner, M., Bushnell, B., Sanderson, K.E. et al. Transductomics: sequencing-based detection analysis transduced DNA pure cultures microbial communities. Microbiome 8, 158 (2020). https://doi.org/10.1186/s40168-020-00935-5","code":""},{"path":"https://jlmaier12.github.io/TrIdent/index.html","id":"input-files","dir":"","previous_headings":"","what":"Input files","title":"TrIdent - Transduction Identification","text":"TrIdent detects read coverage patterns using pattern-matching algorithm operates pileup files. pileup file file format row summarizes ‘pileup’ reads specific genomic locations. Pileup files can used generate rolling mean read coverages associated base pair positions across metagenome assembly reduces data size preserving read coverage patterns. TrIdent requires input pileups files generated using 100 bp window/bin size. read mappers, like BBMap, allow generation pileup files bbmap.sh command use bincov output covbinsize=100 parameter/argument. Otherwise, BBMap’s pileup.sh can convert .bam files produced read mapper pileup files compatible TrIdent using bincov output binsize=100. TrIdent requires two pileup files transductomics dataset input: VLP-fraction pileup: Sequencing reads sample’s ultra-purified VLP-fraction mapped whole-community metagenome assembly sample. whole-community pileup: Sequencing reads sample’s whole-community mapped whole-community metagenome sample. data used pileup file must originate sample. Pileup files must use 100 bp window/bin size rolling mean. Transductomics sample preparation, sequencing procedures, analysis methods detailed Kleiner et al. (2020)","code":""},{"path":"https://jlmaier12.github.io/TrIdent/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"TrIdent - Transduction Identification","text":"Install TrIdent BiocManager: Install development version TrIdent Github BiocManager:","code":"if (!require(\"BiocManager\", quietly = TRUE)) {   install.packages(\"BiocManager\") }  BiocManager::install(\"TrIdent\") library(TrIdent) BiocManager::install(\"jlmaier12/TrIdent\") library(TrIdent)"},{"path":"https://jlmaier12.github.io/TrIdent/index.html","id":"quick-start","dir":"","previous_headings":"","what":"Quick Start","title":"TrIdent - Transduction Identification","text":"","code":"## Load TrIdent library(TrIdent)  ## Load sample datasets data(\"VLPFractionSamplePileup\") data(\"WholeCommunitySamplePileup\")  ## Run TrIdent: ## Run first: TrIdentOutput <- TrIdentClassifier(   VLPpileup = VLPFractionSamplePileup,   WCpileup = WholeCommunitySamplePileup ) #> Reformatting pileup files #> Starting pattern-matching... #> A quarter of the way done with pattern-matching #> Half of the way done with pattern-matching #> Almost done with pattern-matching! #> Determining sizes (bp) of pattern matches #> Identifying highly active/abundant or heterogenously integrated #>       Prophage-like elements #> Finalizing output #> Execution time: 14.56secs #> 1 contigs were filtered out based on low read coverage #> 0 contigs were filtered out based on length #>  #> HighCovNoPattern        NoPattern    Prophage-like          Sloping  #>                1                1                4                3 #> 3 of the prophage-like classifications are highly active or abundant #> 1 of the prophage-like classifications are mixed, i.e. heterogenously #>         integrated into their bacterial host population  ## Run second: plotTrIdentResults(   VLPpileup = VLPFractionSamplePileup,   WCpileup = WholeCommunitySamplePileup,   TrIdentResults = TrIdentOutput ) #> $NODE_62 #>  #> $NODE_135 #>  #> $NODE_1088 #>  #> $NODE_352 #>  #> $NODE_368 #>  #> $NODE_560 #>  #> $NODE_617 #>  #> $NODE_2060 ## Run third: specializedTransductionID(   VLPpileup = VLPFractionSamplePileup,   TrIdentResults = TrIdentOutput ) #> 2 contigs have potential specialized transduction #> We recommend that you also view the results of this search with #>       logScale=TRUE #> $summaryTable #>   contigName specTransduc left right lengthLeft lengthRight #> 1    NODE_62          yes  yes    no      45400        <NA> #> 2   NODE_135           no   no    no       <NA>        <NA> #> 3   NODE_368           no   no    no       <NA>        <NA> #> 4   NODE_617          yes  yes   yes      33300        9800 #>  #> $Plots #> $Plots$NODE_62 #>  #> $Plots$NODE_135 #>  #> $Plots$NODE_368 #>  #> $Plots$NODE_617"},{"path":"https://jlmaier12.github.io/TrIdent/reference/allPatternMatches.html","id":null,"dir":"Reference","previous_headings":"","what":"Collects pattern-match information for all classifications — allPatternMatches","title":"Collects pattern-match information for all classifications — allPatternMatches","text":"Collects pattern information associated contigs classified Prophage-like, Sloping HighCovNoPattern.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/allPatternMatches.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collects pattern-match information for all classifications — allPatternMatches","text":"","code":"allPatternMatches(bestMatchList, classifSummTable)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/allPatternMatches.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collects pattern-match information for all classifications — allPatternMatches","text":"bestMatchList Classifications made patternMatcher function. classifSummTable Classification summary table whole-community:VLP-fraction read coverage ratios calculated.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/allPatternMatches.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collects pattern-match information for all classifications — allPatternMatches","text":"List","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/allProphageLikeClassifs.html","id":null,"dir":"Reference","previous_headings":"","what":"Collects Prophage-like classification pattern-match information — allProphageLikeClassifs","title":"Collects Prophage-like classification pattern-match information — allProphageLikeClassifs","text":"Collects pattern information associated contigs classified Prophage-like.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/allProphageLikeClassifs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collects Prophage-like classification pattern-match information — allProphageLikeClassifs","text":"","code":"allProphageLikeClassifs(bestMatchList)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/allProphageLikeClassifs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collects Prophage-like classification pattern-match information — allProphageLikeClassifs","text":"bestMatchList Classifications made patternMatcher function.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/allProphageLikeClassifs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collects Prophage-like classification pattern-match information — allProphageLikeClassifs","text":"List","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/allSlopingClassifs.html","id":null,"dir":"Reference","previous_headings":"","what":"Collects Sloping classification pattern-match i nformation — allSlopingClassifs","title":"Collects Sloping classification pattern-match i nformation — allSlopingClassifs","text":"Collects pattern information associated contigs classified Sloping patternMatcher function.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/allSlopingClassifs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Collects Sloping classification pattern-match i nformation — allSlopingClassifs","text":"","code":"allSlopingClassifs(bestMatchList)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/allSlopingClassifs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Collects Sloping classification pattern-match i nformation — allSlopingClassifs","text":"bestMatchList Classifications made patternMatcher function.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/allSlopingClassifs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Collects Sloping classification pattern-match i nformation — allSlopingClassifs","text":"List","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/blockBuilder.html","id":null,"dir":"Reference","previous_headings":"","what":"Builds prophage-like block patterns — blockBuilder","title":"Builds prophage-like block patterns — blockBuilder","text":"Build translate block pattern going left side, right side full length contig.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/blockBuilder.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Builds prophage-like block patterns — blockBuilder","text":"","code":"blockBuilder(viralSubset, windowSize, minBlockSize, maxBlockSize)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/blockBuilder.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Builds prophage-like block patterns — blockBuilder","text":"viralSubset subset read coverage pileup pertains contig currently assessed windowSize window size used re-average read coverage pileups minBlockSize minimum size prophage-like block pattern. Default 10000 bp. maxBlockSize maximum size prophage-like block pattern. Default NA.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/blockBuilder.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Builds prophage-like block patterns — blockBuilder","text":"List containing three objects","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/blockTranslator.html","id":null,"dir":"Reference","previous_headings":"","what":"Full block pattern-translator — blockTranslator","title":"Full block pattern-translator — blockTranslator","text":"Translates full block-pattern across contig. Translate pattern 1000 bp time. Stop translating pattern 5000 bp end contig.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/blockTranslator.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Full block pattern-translator — blockTranslator","text":"","code":"blockTranslator(viralSubset, bestMatchInfo, windowSize, pattern)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/blockTranslator.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Full block pattern-translator — blockTranslator","text":"viralSubset subset read coverage pileup pertains contig currently assessed bestMatchInfo information associated current best pattern-match. windowSize window size used re-average read coverage pileups pattern vector containing values associated block pattern","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/blockTranslator.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Full block pattern-translator — blockTranslator","text":"List","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/changeSlope.html","id":null,"dir":"Reference","previous_headings":"","what":"Change slope of sloping pattern — changeSlope","title":"Change slope of sloping pattern — changeSlope","text":"Change value slope used sloping pattern-match","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/changeSlope.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Change slope of sloping pattern — changeSlope","text":"","code":"changeSlope(   leftOrRight,   slopeBottom,   halfToMaxReadCov,   cov,   viralSubset,   windowSize )"},{"path":"https://jlmaier12.github.io/TrIdent/reference/changeSlope.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Change slope of sloping pattern — changeSlope","text":"leftOrRight Generate pattern negative slope (left right, .e. 'Left') positive slope (right left, .e. 'Right') slopeBottom value bottom sloping value halfToMaxReadCov Half max VLP-fraction read coverage divided 10 cov value top slope viralSubset subset read coverage pileup pertains contig currently assessed windowSize window size used re-average read coverage pileup","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/changeSlope.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Change slope of sloping pattern — changeSlope","text":"List","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/changeSlopeWStart.html","id":null,"dir":"Reference","previous_headings":"","what":"Change slope of sloping pattern with initial start — changeSlopeWStart","title":"Change slope of sloping pattern with initial start — changeSlopeWStart","text":"Change value slope used sloping start pattern-match","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/changeSlopeWStart.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Change slope of sloping pattern with initial start — changeSlopeWStart","text":"","code":"changeSlopeWStart(   leftOrRight,   slopeBottom,   slopeBottomChange,   cov,   viralSubset,   windowSize )"},{"path":"https://jlmaier12.github.io/TrIdent/reference/changeSlopeWStart.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Change slope of sloping pattern with initial start — changeSlopeWStart","text":"leftOrRight Generate pattern negative slope (left right, .e. 'Left') positive slope (right left, .e. 'Right') slopeBottom value bottom sloping value slopeBottomChange value used increase bottom slope cov value top slope viralSubset subset read coverage pileup pertains contig currently assessed windowSize window size used re-average read coverage pileup","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/changeSlopeWStart.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Change slope of sloping pattern with initial start — changeSlopeWStart","text":"List","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/changeWindowSize.html","id":null,"dir":"Reference","previous_headings":"","what":"Change the read coverage rolling mean window size — changeWindowSize","title":"Change the read coverage rolling mean window size — changeWindowSize","text":"Re-averages window sizes read coverage averages. Start 100bp windows always. make window size less 100bp.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/changeWindowSize.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Change the read coverage rolling mean window size — changeWindowSize","text":"","code":"changeWindowSize(cleanPileup, windowSize)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/changeWindowSize.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Change the read coverage rolling mean window size — changeWindowSize","text":"cleanPileup read coverage dataset cleaned reformatted. windowSize number base pairs average coverage values . Options 100, 500, 1000, 2000 !","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/changeWindowSize.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Change the read coverage rolling mean window size — changeWindowSize","text":"Dataframe","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/contigClassSumm.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarizes pattern-match information — contigClassSumm","title":"Summarizes pattern-match information — contigClassSumm","text":"Summarizes classifications made patternMatcher() function dataframe.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/contigClassSumm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarizes pattern-match information — contigClassSumm","text":"","code":"contigClassSumm(bestMatchList)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/contigClassSumm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarizes pattern-match information — contigClassSumm","text":"bestMatchList Classifications made patternMatcher function.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/contigClassSumm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarizes pattern-match information — contigClassSumm","text":"dataframe","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/fullSlope.html","id":null,"dir":"Reference","previous_headings":"","what":"Sloping pattern builder — fullSlope","title":"Sloping pattern builder — fullSlope","text":"Build sloping pattern consists sloping line spanning contig assessed. line slopes left right. slope line changed, pattern translated across contig.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/fullSlope.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sloping pattern builder — fullSlope","text":"","code":"fullSlope(viralSubset, windowSize, minSlope)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/fullSlope.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sloping pattern builder — fullSlope","text":"viralSubset subset read coverage pileup pertains contig currently assessed windowSize window size used re-average read coverage pileup minSlope minimum slope value test sloping patterns","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/fullSlope.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sloping pattern builder — fullSlope","text":"List containing two objects","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/leftRightBlockTranslater.html","id":null,"dir":"Reference","previous_headings":"","what":"Translate left and right block patterns across contig — leftRightBlockTranslater","title":"Translate left and right block patterns across contig — leftRightBlockTranslater","text":"Translates left right block patterns across contigs 1000 bp time","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/leftRightBlockTranslater.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Translate left and right block patterns across contig — leftRightBlockTranslater","text":"","code":"leftRightBlockTranslater(   viralSubset,   pattern,   leftOrRight,   windowSize,   minReadCov,   cov,   bestMatchInfo,   minBlockSize )"},{"path":"https://jlmaier12.github.io/TrIdent/reference/leftRightBlockTranslater.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Translate left and right block patterns across contig — leftRightBlockTranslater","text":"viralSubset subset read coverage pileup pertains contig currently assessed pattern pattern vector translated leftOrRight left right block pattern translated windowSize window size used re-average read coverage pileups minReadCov baseline value used region outside block pattern (either 0 minimum VLP-fraction read coverage contig) cov height value currently used block pattern bestMatchInfo information associated current best pattern-match. minBlockSize minimum size Prophage-like block pattern. Default 10,000 bp.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/leftRightBlockTranslater.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Translate left and right block patterns across contig — leftRightBlockTranslater","text":"List","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/makeBlockPattern.html","id":null,"dir":"Reference","previous_headings":"","what":"Make block patterns for pattern-matching — makeBlockPattern","title":"Make block patterns for pattern-matching — makeBlockPattern","text":"Make full, left right block patterns Prophage-like classifications","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/makeBlockPattern.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make block patterns for pattern-matching — makeBlockPattern","text":"","code":"makeBlockPattern(   viralSubset,   windowSize,   fullLeftRight,   blockLength,   nonBlock,   minReadCov,   cov )"},{"path":"https://jlmaier12.github.io/TrIdent/reference/makeBlockPattern.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make block patterns for pattern-matching — makeBlockPattern","text":"viralSubset subset read coverage pileup pertains contig currently assessed windowSize window size used re-average read coverage pileups fullLeftRight block pattern variation built blockLength Maximum block pattern length nonBlock Maximum non-block pattern length minReadCov Either 0 minimum VLP-fraction read coverage value cov height value block pattern","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/makeBlockPattern.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make block patterns for pattern-matching — makeBlockPattern","text":"List containing two objects","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/makeFullSlopes.html","id":null,"dir":"Reference","previous_headings":"","what":"Make full slope patterns — makeFullSlopes","title":"Make full slope patterns — makeFullSlopes","text":"Makes slope patterns sloping either left right (Left) right left (right) across contig assessed.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/makeFullSlopes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make full slope patterns — makeFullSlopes","text":"","code":"makeFullSlopes(leftOrRight, viralSubset, newMax, minReadCov, windowSize)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/makeFullSlopes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make full slope patterns — makeFullSlopes","text":"leftOrRight Generate pattern negative slope (left right, .e. 'Left') positive slope (right left, .e. 'Right') viralSubset subset read coverage pileup pertains contig currently assessed newMax value top sloping pattern slightly higher maximum coverage value viralSubset minReadCov Minimum read coverage value viralSubset windowSize window size used re-average read coverage pileups","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/makeFullSlopes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make full slope patterns — makeFullSlopes","text":"List","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/makeSlopesWStarts.html","id":null,"dir":"Reference","previous_headings":"","what":"Make slope patterns with starts — makeSlopesWStarts","title":"Make slope patterns with starts — makeSlopesWStarts","text":"Makes slope patterns sloping either left right (Left) right left (right) across contig assessed. Slope patterns contain initiation point.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/makeSlopesWStarts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make slope patterns with starts — makeSlopesWStarts","text":"","code":"makeSlopesWStarts(leftOrRight, viralSubset, newMax, minReadCov, windowSize)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/makeSlopesWStarts.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make slope patterns with starts — makeSlopesWStarts","text":"leftOrRight Generate pattern negative slope (left right, .e. 'Left') positive slope (right left, .e. 'Right') viralSubset subset read coverage pileup pertains contig currently assessed newMax value top sloping pattern slightly higher maximum coverage value viralSubset minReadCov Minimum read coverage value viralSubset windowSize window size used re-average read coverage pileup","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/makeSlopesWStarts.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make slope patterns with starts — makeSlopesWStarts","text":"List","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/NARemover.html","id":null,"dir":"Reference","previous_headings":"","what":"NA remover — NARemover","title":"NA remover — NARemover","text":"Removes NAs dataframe.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/NARemover.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"NA remover — NARemover","text":"","code":"NARemover(x)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/NARemover.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"NA remover — NARemover","text":"x dataset potential NAs","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/NARemover.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"NA remover — NARemover","text":"Dataframe","code":""},{"path":[]},{"path":"https://jlmaier12.github.io/TrIdent/reference/noPattern.html","id":null,"dir":"Reference","previous_headings":"","what":"No pattern pattern-match — noPattern","title":"No pattern pattern-match — noPattern","text":"horizontal line mean median coverage optimal pattern-match contig read coverage displays sloping block patterns","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/noPattern.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"No pattern pattern-match — noPattern","text":"","code":"noPattern(viralSubset)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/noPattern.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"No pattern pattern-match — noPattern","text":"viralSubset subset read coverage pileup pertains contig currently assessed","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/noPattern.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"No pattern pattern-match — noPattern","text":"List","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/patternBuilder.html","id":null,"dir":"Reference","previous_headings":"","what":"Pattern-builder — patternBuilder","title":"Pattern-builder — patternBuilder","text":"Builds pattern (vector) associated best pattern-match' contig classified Prophage-like, Sloping, HighCovNoPattern.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/patternBuilder.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pattern-builder — patternBuilder","text":"","code":"patternBuilder(viralSubset, classifList, classification, i)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/patternBuilder.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pattern-builder — patternBuilder","text":"viralSubset subset read coverage pileup pertains contig currently assessed classifList list containing pattern match information associated classified contigs. classification contig's classification assigned TrIdentClassifier function list index associated contig's pattern-match information","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/patternBuilder.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pattern-builder — patternBuilder","text":"Vector","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/patternMatcher.html","id":null,"dir":"Reference","previous_headings":"","what":"Main pattern-matching function — patternMatcher","title":"Main pattern-matching function — patternMatcher","text":"Creates viralSubset, representative one contig, used input individual pattern-matching function. information associated best match pattern obtained, pattern smallest match score used classify contig assessed. Prior pattern-matching, contigs smaller minContigLength contigs without 5,000 bp 10x read coverage removed.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/patternMatcher.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Main pattern-matching function — patternMatcher","text":"","code":"patternMatcher(   VLPpileup,   WCpileup,   windowSize,   minBlockSize,   maxBlockSize,   minContigLength,   minSlope )"},{"path":"https://jlmaier12.github.io/TrIdent/reference/patternMatcher.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Main pattern-matching function — patternMatcher","text":"VLPpileup table containing contig names, coverages averaged 100 bp windows, contig positions associated mapping VLP-fraction reads whole-community contigs WCpileup table containing contig names, coverages averaged 100 bp windows, contig positions associated mapping whole-community reads whole-community contigs windowSize window size used re-average read coverage datasets minBlockSize minimum size prophage-like block pattern. Default 10,000 bp. maxBlockSize maximum size prophage-like block pattern. Default NA minContigLength minimum contig size (bp) perform pattern-matching . Must least 20,000 bp. Default 30,000 bp. minSlope minimum slope value test sloping patterns","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/patternMatcher.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Main pattern-matching function — patternMatcher","text":"List containing three objects.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/patternMatchSize.html","id":null,"dir":"Reference","previous_headings":"","what":"Pattern-match size calculator — patternMatchSize","title":"Pattern-match size calculator — patternMatchSize","text":"Calculate size (bp) matching region Prophage-like Sloping patterns","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/patternMatchSize.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pattern-match size calculator — patternMatchSize","text":"","code":"patternMatchSize(classifSumm, classifList, windowSize, verbose)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/patternMatchSize.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pattern-match size calculator — patternMatchSize","text":"classifSumm Classification summary table classifList list containing pattern match information associated contig classifications windowSize window size used re-average read coverage pileups verbose TRUE FALSE. Print progress messages console. Default TRUE.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/patternMatchSize.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pattern-match size calculator — patternMatchSize","text":"dataframe","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/pileupFormatter.html","id":null,"dir":"Reference","previous_headings":"","what":"Correctly formats pileup files. — pileupFormatter","title":"Correctly formats pileup files. — pileupFormatter","text":"Places columns correct order renames columns. Cleans contig labels remove excess information whitespace.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/pileupFormatter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Correctly formats pileup files. — pileupFormatter","text":"","code":"pileupFormatter(pileup)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/pileupFormatter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Correctly formats pileup files. — pileupFormatter","text":"pileup table containing contig names, read coverages averaged 100 bp windows,contig positions","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/pileupFormatter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Correctly formats pileup files. — pileupFormatter","text":"dataframe","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/plotTrIdentResults.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot read coverage graphs of contigs classified as Prophage-like, Sloping, or HighCovNoPattern — plotTrIdentResults","title":"Plot read coverage graphs of contigs classified as Prophage-like, Sloping, or HighCovNoPattern — plotTrIdentResults","text":"Plot read coverages contig associated pattern-match Prophage-like, Sloping HighCovNoPattern classifications. Returns list ggplot objects.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/plotTrIdentResults.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot read coverage graphs of contigs classified as Prophage-like, Sloping, or HighCovNoPattern — plotTrIdentResults","text":"","code":"plotTrIdentResults(   VLPpileup,   WCpileup,   TrIdentResults,   matchScoreFilter,   saveFilesTo )"},{"path":"https://jlmaier12.github.io/TrIdent/reference/plotTrIdentResults.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot read coverage graphs of contigs classified as Prophage-like, Sloping, or HighCovNoPattern — plotTrIdentResults","text":"VLPpileup VLP-fraction pileup file generated mapping sequencing reads sample's ultra-purified VLP-fraction mapped sample's whole-community metagenome assembly. pileup file MUST following format: * V1: Contig accession * V2: Mapped read coverage values averaged 100 bp windows * V3: Starting position (bp) 100 bp window. Restarts 0 start new contig. * V4: Starting position (bp) 100 bp window. restart start new contig. WCpileup whole-community pileup file generated mapping sequencing reads sample's whole-community mapped sample's whole-community metagenome assembly. pileup file MUST following format: * V1: Contig accession * V2: Mapped read coverage values averaged 100 bp windows * V3: Starting position (bp) 100 bp window. Restarts 0 start new contig. * V4: Starting position (bp) 100 bp window. restart start new contig. TrIdentResults Output `TrIdentClassifier()`. matchScoreFilter Optional, Filter plots using normalized pattern match-scores. suggested filtering threshold provided `TrIdentClassifier()` `suggFiltThresh=TRUE`. saveFilesTo Optional, Provide path directory wish save output . folder made within provided directory store results.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/plotTrIdentResults.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot read coverage graphs of contigs classified as Prophage-like, Sloping, or HighCovNoPattern — plotTrIdentResults","text":"Large list containing ggplot objects","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/plotTrIdentResults.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot read coverage graphs of contigs classified as Prophage-like, Sloping, or HighCovNoPattern — plotTrIdentResults","text":"","code":"data(\"VLPFractionSamplePileup\") data(\"WholeCommunitySamplePileup\") data(\"TrIdentSampleOutput\")  patternMatches <- plotTrIdentResults(   VLPpileup = VLPFractionSamplePileup,   WCpileup = WholeCommunitySamplePileup,   TrIdentResults = TrIdentSampleOutput )"},{"path":"https://jlmaier12.github.io/TrIdent/reference/prophageLikeBorders.html","id":null,"dir":"Reference","previous_headings":"","what":"Prophage-like border finder — prophageLikeBorders","title":"Prophage-like border finder — prophageLikeBorders","text":"Find borders Prophage-like patterns specificity pattern-matching using 100 bp window pileups sliding standard deviation technique.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/prophageLikeBorders.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prophage-like border finder — prophageLikeBorders","text":"","code":"prophageLikeBorders(viralSubset, classificationPatterns, i, windowSize)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/prophageLikeBorders.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prophage-like border finder — prophageLikeBorders","text":"viralSubset subset read coverage pileup pertains contig currently assessed classificationPatterns pattern match information associated contig classified Prophage-like, Sloping, HighCovNoPattern index contig currently assessed windowSize window size used re-average read coverage pileups","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/prophageLikeBorders.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prophage-like border finder — prophageLikeBorders","text":"List","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/prophageLikeElevation.html","id":null,"dir":"Reference","previous_headings":"","what":"Determine Prophage-like read coverage elevation in whole-community — prophageLikeElevation","title":"Determine Prophage-like read coverage elevation in whole-community — prophageLikeElevation","text":"Determines whether detected Prophage-like genetic element read coverage whole-community either elevated depressed compared average read coverage non-prophage region.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/prophageLikeElevation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determine Prophage-like read coverage elevation in whole-community — prophageLikeElevation","text":"","code":"prophageLikeElevation(   classifSummTable,   prophageLikeClassifList,   VLPpileup,   WCpileup,   windowSize,   verbose )"},{"path":"https://jlmaier12.github.io/TrIdent/reference/prophageLikeElevation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determine Prophage-like read coverage elevation in whole-community — prophageLikeElevation","text":"classifSummTable Classification summary table prophageLikeClassifList list containing pattern match information associated contigs classified Prophage-like. VLPpileup table containing contig names, coverages averaged 100 bp windows, contig positions associated mapping VLP-fraction reads whole-community contigs WCpileup table containing contig names, coverages averaged 100 bp windows, contig positions associated mapping whole-community reads whole-community contigs windowSize window size used re-average read coverage pileups verbose TRUE FALSE. Print progress messages console. Default TRUE.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/prophageLikeElevation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determine Prophage-like read coverage elevation in whole-community — prophageLikeElevation","text":"dataframe","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/prophageLikeZoom.html","id":null,"dir":"Reference","previous_headings":"","what":"Prophage-like pattern zoom — prophageLikeZoom","title":"Prophage-like pattern zoom — prophageLikeZoom","text":"'Zoom-' (aka subset) desired region surrounding block pattern.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/prophageLikeZoom.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prophage-like pattern zoom — prophageLikeZoom","text":"","code":"prophageLikeZoom(viralSubset, classificationPatterns, i, zoom, windowSize)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/prophageLikeZoom.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prophage-like pattern zoom — prophageLikeZoom","text":"viralSubset subset read coverage pileup pertains contig currently assessed classificationPatterns pattern match information associated contig classified Prophage-like, sloping, HighCovNoPattern index contig currently assessed zoom number rows outside start stop positions block pattern zoom-windowSize window size used re-average read coverage pileups","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/prophageLikeZoom.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prophage-like pattern zoom — prophageLikeZoom","text":"Dataframe","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/resultsHisto.html","id":null,"dir":"Reference","previous_headings":"","what":"Create histogram of normalized pattern-match scores — resultsHisto","title":"Create histogram of normalized pattern-match scores — resultsHisto","text":"Plots histogram normalized match scores Prophage-like, Sloping HighCovNoPattern classifications colors plot based classifications. suggested filtering threshold provided filtering results based quality pattern-match.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/resultsHisto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create histogram of normalized pattern-match scores — resultsHisto","text":"","code":"resultsHisto(summaryList, suggFiltThresh)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/resultsHisto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create histogram of normalized pattern-match scores — resultsHisto","text":"summaryList Classification summary table filtered include contigs Prophage-like, Sloping HighCovNoPattern classifications suggFiltThresh TRUE FALSE, Suggest filtering threshold output pattern-match score histogram. Default FALSE.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/resultsHisto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create histogram of normalized pattern-match scores — resultsHisto","text":"ggplot object","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/slopeSumm.html","id":null,"dir":"Reference","previous_headings":"","what":"Summarize slopes for sloping classifications — slopeSumm","title":"Summarize slopes for sloping classifications — slopeSumm","text":"Add slope information sloping classifications summary table","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/slopeSumm.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summarize slopes for sloping classifications — slopeSumm","text":"","code":"slopeSumm(classifSumm, slopingClassifList, windowSize)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/slopeSumm.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summarize slopes for sloping classifications — slopeSumm","text":"classifSumm Classification summary table slopingClassifList list containing pattern match information associated contigs classified sloping. windowSize window size used re-average read coverage pileups","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/slopeSumm.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summarize slopes for sloping classifications — slopeSumm","text":"dataframe","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/slopeTranslator.html","id":null,"dir":"Reference","previous_headings":"","what":"Sloping pattern translator — slopeTranslator","title":"Sloping pattern translator — slopeTranslator","text":"Translates sloping pattern containing initial jump-read coverage across contig. Translate pattern 1000 bp time. Stop translating pattern left contig reaches 20,000 bp.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/slopeTranslator.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sloping pattern translator — slopeTranslator","text":"","code":"slopeTranslator(   viralSubset,   bestMatchInfo,   windowSize,   slopeChange,   leftOrRight )"},{"path":"https://jlmaier12.github.io/TrIdent/reference/slopeTranslator.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sloping pattern translator — slopeTranslator","text":"viralSubset subset read coverage pileup pertains contig currently assessed bestMatchInfo pattern-match information associated current best pattern match. windowSize window size used re-average read coverage pileups slopeChange list containing pattern vector, slope value, value slope bottom leftOrRight direction sloping pattern. Either \"Left\" left right (neg) slopes \"Right\" right left (pos) slopes.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/slopeTranslator.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sloping pattern translator — slopeTranslator","text":"List","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/slopeWithStart.html","id":null,"dir":"Reference","previous_headings":"","what":"Sloping pattern with an initial jump-up in read coverage — slopeWithStart","title":"Sloping pattern with an initial jump-up in read coverage — slopeWithStart","text":"Build, translate, change slope sloping pattern slope start","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/slopeWithStart.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sloping pattern with an initial jump-up in read coverage — slopeWithStart","text":"","code":"slopeWithStart(viralSubset, windowSize, minSlope)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/slopeWithStart.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sloping pattern with an initial jump-up in read coverage — slopeWithStart","text":"viralSubset subset read coverage pileup pertains contig currently assessed windowSize window size used re-average read coverage pileups minSlope minimum slope value test sloping patterns","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/slopeWithStart.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sloping pattern with an initial jump-up in read coverage — slopeWithStart","text":"List containing two objects","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/specializedTransductionID.html","id":null,"dir":"Reference","previous_headings":"","what":"Identify potential specialized transduction events on contigs classified as Prophage-like — specializedTransductionID","title":"Identify potential specialized transduction events on contigs classified as Prophage-like — specializedTransductionID","text":"Search contigs classified Prophage-like dense read coverage outside pattern-match borders may indicate specialized transduction. Returns list first object containing summary table second object containing list plots associated specialzied transduction search results. plot green, identified potential specialized transduction.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/specializedTransductionID.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Identify potential specialized transduction events on contigs classified as Prophage-like — specializedTransductionID","text":"","code":"specializedTransductionID(   VLPpileup,   TrIdentResults,   specificContig,   noReadCov = 500,   specTransLength = 2000,   matchScoreFilter,   logScale = FALSE,   verbose = TRUE,   SaveFilesTo )"},{"path":"https://jlmaier12.github.io/TrIdent/reference/specializedTransductionID.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Identify potential specialized transduction events on contigs classified as Prophage-like — specializedTransductionID","text":"VLPpileup VLP-fraction pileup file generated mapping sequencing reads sample's ultra-purified VLP-fraction mapped sample's whole-community metagenome assembly. pileup file MUST following format: * V1: Contig accession * V2: Mapped read coverage values averaged 100 bp windows * V3: Starting position (bp) 100 bp window. Restarts 0 start new contig. * V4: Starting position (bp) 100 bp window. restart start new contig. TrIdentResults Output `TrIdentClassifier()` specificContig Optional, Search specific contig classified Prophage-like (\"NODE_1\"). noReadCov Number basepairs zero read coverage encountered specialized transduction searching stops. Default 500. Must least 100. specTransLength Number basepairs non-zero read coverage needed specialized transduction considered. Default 2000. Must least 100. matchScoreFilter Optional, Filter plots using normalized pattern match-scores. suggested filtering threshold provided `TrIdentClassifier()` `suggFiltThresh=TRUE`. logScale TRUE FALSE, display VLP-fraction read coverage log10 scale. Default FALSE. verbose TRUE FALSE. Print progress messages console. Default TRUE. SaveFilesTo Provide path directory wish save output . `specializedTransductionID()` make folder within provided directory store results.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/specializedTransductionID.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Identify potential specialized transduction events on contigs classified as Prophage-like — specializedTransductionID","text":"Large list containing two objects","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/specializedTransductionID.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Identify potential specialized transduction events on contigs classified as Prophage-like — specializedTransductionID","text":"","code":"data(\"VLPFractionSamplePileup\") data(\"TrIdentSampleOutput\")  specTransduction <- specializedTransductionID(   VLPpileup = VLPFractionSamplePileup,   TrIdentResults = TrIdentSampleOutput ) #> 2 contigs have potential specialized transduction #> We recommend that you also view the results of this search with #>       logScale=TRUE  specTransductionNODE62 <- specializedTransductionID(   VLPpileup = VLPFractionSamplePileup,   TrIdentResults = TrIdentSampleOutput,   specificContig = \"NODE_62\" ) #> 1 contigs have potential specialized transduction #> We recommend that you also view the results of this search with #>       logScale=TRUE"},{"path":"https://jlmaier12.github.io/TrIdent/reference/specTransductionPlot.html","id":null,"dir":"Reference","previous_headings":"","what":"Specialized transduction plot — specTransductionPlot","title":"Specialized transduction plot — specTransductionPlot","text":"Plot search results `specializedTransductionID()`","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/specTransductionPlot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Specialized transduction plot — specTransductionPlot","text":"","code":"specTransductionPlot(   viralSubsetZoom,   startPosBp,   endPosBp,   SpecTransLeft,   specTransRight,   contigName,   classifPatternMatches,   i,   specTransSumm,   logScale,   classifSumm )"},{"path":"https://jlmaier12.github.io/TrIdent/reference/specTransductionPlot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Specialized transduction plot — specTransductionPlot","text":"viralSubsetZoom contig subset surrounding Prophage-like pattern-match startPosBp Left border position endPosBp Right border position SpecTransLeft End position spec transduction left border specTransRight End position spec transduction right border contigName reference name contig currently assessed (.e \"NODE_1\") classifPatternMatches pattern match information associated contig classified prophage-like,  sloping, HighCovNoPattern index contig currently assessed specTransSumm Results spec transduction search logScale TRUE, coverage plotted log10. FALSE, raw coverage values plotted. Default FALSE. classifSumm summary information associated contig classified Prophage-like, Sloping, HighCovNoPattern","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/specTransductionPlot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Specialized transduction plot — specTransductionPlot","text":"ggplot object","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/specTransductionSearch.html","id":null,"dir":"Reference","previous_headings":"","what":"Specialized transduction search and plot — specTransductionSearch","title":"Specialized transduction search and plot — specTransductionSearch","text":"Search contigs classified prophage-like potential specialized transduction return plot visualizing search results.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/specTransductionSearch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Specialized transduction search and plot — specTransductionSearch","text":"","code":"specTransductionSearch(   contigName,   VLPpileup,   classifPatternMatches,   classifSumm,   windowSize,   i,   noReadCov,   specTransLength,   logScale )"},{"path":"https://jlmaier12.github.io/TrIdent/reference/specTransductionSearch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Specialized transduction search and plot — specTransductionSearch","text":"contigName reference name contig currently assessed (.e \"NODE_1\") VLPpileup table containing contig names, coverages averaged 100 bp windows, contig positions associated mapping VLP-fraction reads whole-community contigs classifPatternMatches pattern match information associated contig classified prophage-like,  sloping, HighCovNoPattern classifSumm summary information associated contig classified Prophage-like, Sloping, HighCovNoPattern windowSize window size used re-average read coverage pileups index contig currently assessed noReadCov many bp read coverage encountered searching stops? Default 500. specTransLength many bp read coverage look outside prophage borders? Default 2000. logScale TRUE, coverage plotted log10. FALSE, raw coverage values plotted. Default FALSE.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/specTransductionSearch.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Specialized transduction search and plot — specTransductionSearch","text":"List containing two objects","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/TrIdent-package.html","id":null,"dir":"Reference","previous_headings":"","what":"TrIdent - Transduction Identification — TrIdent-package","title":"TrIdent - Transduction Identification — TrIdent-package","text":"Automatic detection, classification characterization   transduction events transductomics datasets using read coverage   pattern-matching. Please see [Transductomics: sequencing-based detection analysis transduced DNA pure cultures microbial communities] (   https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-020-00935-5)   information transductomics method, data analysis   workflow.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/TrIdent-package.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"TrIdent - Transduction Identification — TrIdent-package","text":"three main functions TrIdent : TrIdentClassifier performs pattern-matching, classification characterization read coverage patterns contigs. plotTrIdentResults plots results  TrIdentClassifier() specializedTransductionID searches contigs classified Prophage-like TrIdentClassifier() potential specialized transduction","code":""},{"path":[]},{"path":"https://jlmaier12.github.io/TrIdent/reference/TrIdent-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"TrIdent - Transduction Identification — TrIdent-package","text":"Jessie Maier jlmaier@ncsu.edu & Jorden Rabasco   jrabasc@ncsu.edu","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/TrIdentClassifier.html","id":null,"dir":"Reference","previous_headings":"","what":"Classify contigs as Prophage-like, Sloping, HighCovNoPattern, and NoPattern — TrIdentClassifier","title":"Classify contigs as Prophage-like, Sloping, HighCovNoPattern, and NoPattern — TrIdentClassifier","text":"Performs pattern-matching summarizes results list. first item list table consisting summary information contigs passed pattern-matching (.e filtered ). second item list table consisting summary information contigs classified via pattern-matching. third item list contains pattern-match information associated contig previous table. fourth object list table containing contigs filtered prior pattern-matching. fifth item windowSize used search.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/TrIdentClassifier.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Classify contigs as Prophage-like, Sloping, HighCovNoPattern, and NoPattern — TrIdentClassifier","text":"","code":"TrIdentClassifier(   VLPpileup,   WCpileup,   windowSize = 1000,   minBlockSize = 10000,   maxBlockSize = Inf,   minContigLength = 30000,   minSlope = 0.001,   suggFiltThresh = FALSE,   verbose = TRUE,   SaveFilesTo )"},{"path":"https://jlmaier12.github.io/TrIdent/reference/TrIdentClassifier.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Classify contigs as Prophage-like, Sloping, HighCovNoPattern, and NoPattern — TrIdentClassifier","text":"VLPpileup VLP-fraction pileup file generated mapping sequencing reads sample's ultra-purified VLP-fraction mapped sample's whole-community metagenome assembly. pileup file MUST following format: * V1: Contig accession * V2: Mapped read coverage values averaged 100 bp windows * V3: Starting position (bp) 100 bp window. Restarts 0 start new contig. * V4: Starting position (bp) 100 bp window. restart start new contig. WCpileup whole-community pileup file generated mapping sequencing reads sample's whole-community mapped sample's whole-community metagenome assembly. pileup file MUST following format: * V1: Contig accession * V2: Mapped read coverage values averaged 100 bp windows * V3: Starting position (bp) 100 bp window. Restarts 0 start new contig. * V4: Starting position (bp) 100 bp window. restart start new contig. windowSize number basepairs average read coverage values . Options 100, 200, 500, 1000 .  Default 1000. minBlockSize minimum size (bp) Prophage-like block pattern. Default 10000. Must least 1000. maxBlockSize maximum size (bp) Prophage-like block pattern. Default NA (maximum). minContigLength minimum contig size (bp) perform pattern-matching . Must least 25000. Default 30000. minSlope minimum slope value test sloping patterns. Default 0.001 (.e minimum change 10x read coverage 100,000 bp). suggFiltThresh TRUE FALSE, Suggest filtering threshold TrIdent classifications based normalized pattern-match scores. Default FALSE. verbose TRUE FALSE. Print progress messages console. Default TRUE. SaveFilesTo Optional, Provide path directory wish save output . folder made within provided directory store results.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/TrIdentClassifier.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Classify contigs as Prophage-like, Sloping, HighCovNoPattern, and NoPattern — TrIdentClassifier","text":"Large list containing 5 objects","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/TrIdentClassifier.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Classify contigs as Prophage-like, Sloping, HighCovNoPattern, and NoPattern — TrIdentClassifier","text":"","code":"data(\"VLPFractionSamplePileup\") data(\"WholeCommunitySamplePileup\")  TrIdent_results <- TrIdentClassifier(   VLPpileup = VLPFractionSamplePileup,   WCpileup = WholeCommunitySamplePileup ) #> Reformatting pileup files #> Starting pattern-matching... #> A quarter of the way done with pattern-matching #> Half of the way done with pattern-matching #> Almost done with pattern-matching! #> Determining sizes (bp) of pattern matches #> Identifying highly active/abundant or heterogenously integrated #>       Prophage-like elements #> Finalizing output #> Execution time: 27.2secs #> 1 contigs were filtered out based on low read coverage #> 0 contigs were filtered out based on length #>  #> HighCovNoPattern        NoPattern    Prophage-like          Sloping  #>                1                1                4                3  #> 3 of the prophage-like classifications are highly active or abundant #> 1 of the prophage-like classifications are mixed, i.e. heterogenously #>         integrated into their bacterial host population"},{"path":"https://jlmaier12.github.io/TrIdent/reference/TrIdentSampleOutput.html","id":null,"dir":"Reference","previous_headings":"","what":"TrIdentSampleOutput — TrIdentSampleOutput","title":"TrIdentSampleOutput — TrIdentSampleOutput","text":"TrIdentClassifier output VLPFractionSamplePileup WholeCommunitySamplePileup files run default parameters Report...","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/TrIdentSampleOutput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"TrIdentSampleOutput — TrIdentSampleOutput","text":"","code":"data('TrIdentSampleOutput')"},{"path":"https://jlmaier12.github.io/TrIdent/reference/TrIdentSampleOutput.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"TrIdentSampleOutput — TrIdentSampleOutput","text":"## 'TrIdentSampleOutput' list 6 objects: SummaryTable dataframe containing classifications    contigs processed pattern-matching CleanedSummaryTable SummaryTable dataframe filtered remove    contigs recieved 'None' classification PatternMatchInfo list lists containing pattern-match    information classified contig FilteredOutContigTable dataframe containing names contigs    filtered prior pattern-matching windowSize windowSize used TrIdentClassifier function (1000) ResultHistogram histogram displaying overall abundance    quality pattern-matches addition composition    classifications. displayed pattern-match scores normalized    dividing score associated contig length. scores    normalized visualize overall quality pattern-matching    entire dataset.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/TrIdentSampleOutput.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"TrIdentSampleOutput — TrIdentSampleOutput","text":"list object produced TrIdentClassifier function run VLPFractionSamplePileup WholeCommunitySamplePileup files run default parameters","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/VLPFractionSamplePileup.html","id":null,"dir":"Reference","previous_headings":"","what":"VLP-Fraction of Sample Dataset — VLPFractionSamplePileup","title":"VLP-Fraction of Sample Dataset — VLPFractionSamplePileup","text":"subset contigs raw VLP-fraction read coverage pileup file generated BBMap's pileup.sh. Report...","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/VLPFractionSamplePileup.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"VLP-Fraction of Sample Dataset — VLPFractionSamplePileup","text":"","code":"data('VLPFractionSamplePileup')"},{"path":"https://jlmaier12.github.io/TrIdent/reference/VLPFractionSamplePileup.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"VLP-Fraction of Sample Dataset — VLPFractionSamplePileup","text":"## 'VLPFractionSamplePileup' data frame 10,805 rows 4   columns: V1 Contig accession V2 Mapped read coverage averaged 100 bp window size V3 Starting position (bp) 100 bp window. Restarts 0  start new contig. V4 Starting position (bp) 100 bp window. restart  start new contig.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/VLPFractionSamplePileup.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"VLP-Fraction of Sample Dataset — VLPFractionSamplePileup","text":"<https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-020-00935-5>","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/VLPFractionSamplePileup.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"VLP-Fraction of Sample Dataset — VLPFractionSamplePileup","text":"dataset represents one half complete transductomics dataset comprised two parts-whole-community fraction viral-like particle (VLP)-fraction. dataset represents VLP fraction generated purifying VLPs conventional mouse fecal homogenate using CsCl density gradient ultracentrifugation. VLP-fraction extracted DNA sequenced Illumina (paired-end mode, 150 bp reads) sequencing reads mapped associated whole-community assembly using BBMap. bbmap.sh bincov parameter covbinsize=100 used create pileup file 100 bp windows. subset 10 contigs pileup file selected sample dataset. contigs chosen associated read coverage patterns VLP-fraction exemplify TrIdent's pattern-matching functionality across classifications: NODE_617:Prophage-like, active/abundant, spec transduction NODE_135:Prophage-like, one side contig, spec transduction NODE_352:Sloping, left right slope NODE_1088: Sloping, right left slope NODE_2060: Sloping, right left slope start NODE_1401: None, pattern match NODE_62: Prophage-like, spec transduction NODE_368: Prophage-like, homogeneously integrated/present, spec transduction NODE_560: HighCovNoPattern NODE_1165: None, filtered access sequencing data used generate pileup file additional details assembly mapping parameters, refer reference : Reference: Kleiner, M., Bushnell, B., Sanderson, K.E. et al. Transductomics: sequencing-based detection analysis transduced DNA pure cultures microbial communities. Microbiome 8, 158 (2020). https://doi.org/10.1186/s40168-020-00935-5","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/VLPtoWCRatioCalc.html","id":null,"dir":"Reference","previous_headings":"","what":"VLP-fraction:whole-community read coverage ratio calculator — VLPtoWCRatioCalc","title":"VLP-fraction:whole-community read coverage ratio calculator — VLPtoWCRatioCalc","text":"Calculate VLP-fraction:whole-community read coverage ratio every contig using median read coverage values. ratio greater 2 (.e VLP-fraction read coverage , average, least double whole-community read coverage), contig classified HighCovNoPattern","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/VLPtoWCRatioCalc.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"VLP-fraction:whole-community read coverage ratio calculator — VLPtoWCRatioCalc","text":"","code":"VLPtoWCRatioCalc(classifSumm, WCpileup, VLPpileup)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/VLPtoWCRatioCalc.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"VLP-fraction:whole-community read coverage ratio calculator — VLPtoWCRatioCalc","text":"classifSumm Classification summary table WCpileup table containing contig names, coverages averaged 100 bp windows, contig positions associated mapping whole-community reads whole-community contigs VLPpileup table containing contig names, coverages averaged 100 bp windows, contig positions associated mapping VLP-fraction reads whole-community contigs","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/VLPtoWCRatioCalc.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"VLP-fraction:whole-community read coverage ratio calculator — VLPtoWCRatioCalc","text":"dataframe","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/WholeCommunitySamplePileup.html","id":null,"dir":"Reference","previous_headings":"","what":"Whole-Community Fraction of Sample Dataset — WholeCommunitySamplePileup","title":"Whole-Community Fraction of Sample Dataset — WholeCommunitySamplePileup","text":"subset contigs raw whole-community fraction read coverage pileup file generated read mapping. Report...","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/WholeCommunitySamplePileup.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Whole-Community Fraction of Sample Dataset — WholeCommunitySamplePileup","text":"","code":"data('WholeCommunitySamplePileup')"},{"path":"https://jlmaier12.github.io/TrIdent/reference/WholeCommunitySamplePileup.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Whole-Community Fraction of Sample Dataset — WholeCommunitySamplePileup","text":"## 'WholeCommunitySamplePileup' data frame 10,805 rows 4   columns: V1 Contig accession V2 Mapped read coverage averaged 100 bp window size V3 Starting position (bp) 100 bp window. Restarts 0  start new contig. V4 Starting position (bp) 100 bp window. restart  start new contig.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/WholeCommunitySamplePileup.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Whole-Community Fraction of Sample Dataset — WholeCommunitySamplePileup","text":"<https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-020-00935-5>","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/WholeCommunitySamplePileup.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Whole-Community Fraction of Sample Dataset — WholeCommunitySamplePileup","text":"dataset represents one half complete transductomics dataset comprised two parts-whole-community fraction viral-like particle (VLP)-fraction. dataset represents whole-community fraction generated conventional mouse fecal homogenate. whole-community extracted DNA sequenced Illumina (paired-end mode, 150 bp reads) metagenome assembled. sequencing reads mapped assembled contigs using BBMap. bbmap.sh bincov parameter covbinsize=100 used create pileup file 100 bp windows. subset 10 contigs pileup file selected sample dataset. contigs chosen associated read coverage patterns VLP-fraction exemplify TrIdent's pattern-matching characterization functionality across classifications: NODE_617:Prophage-like, active/abundant, spec transduction NODE_135:Prophage-like, one side contig, spec transduction NODE_352:Sloping, left right slope NODE_1088: Sloping, right left slope NODE_2060: Sloping, right left slope start NODE_1401: None, pattern match NODE_62: Prophage-like, spec transduction NODE_368: Prophage-like, homogeneously integrated/present, spec transduction NODE_560: HighCovNoPattern NODE_1165: None, filtered access sequencing data used generate pileup file additional details assembly mapping parameters, refer reference : Reference: Kleiner, M., Bushnell, B., Sanderson, K.E. et al. Transductomics: sequencing-based detection analysis transduced DNA pure cultures microbial communities. Microbiome 8, 158 (2020). https://doi.org/10.1186/s40168-020-00935-5","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/zeroCountSearch.html","id":null,"dir":"Reference","previous_headings":"","what":"Counts zero values to the left and right of prophage-like borders — zeroCountSearch","title":"Counts zero values to the left and right of prophage-like borders — zeroCountSearch","text":"Checks see point number consecutive zero values left right prophage-like pattern match borders equals noReadCov parameter","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/zeroCountSearch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Counts zero values to the left and right of prophage-like borders — zeroCountSearch","text":"","code":"zeroCountSearch(startOrEnd, viralSubsetZoom, startOrEndPosRow, noReadCov)"},{"path":"https://jlmaier12.github.io/TrIdent/reference/zeroCountSearch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Counts zero values to the left and right of prophage-like borders — zeroCountSearch","text":"startOrEnd searching start (left side) end (right side) prophage-like pattern-match viralSubsetZoom viralSubset dataframe subsetted 50,000 bp outside pattern match borders startOrEndPosRow row index start end position prophage-like pattern match noReadCov many bp read coverage encountered specialized transduction searching stops? Default 500.","code":""},{"path":"https://jlmaier12.github.io/TrIdent/reference/zeroCountSearch.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Counts zero values to the left and right of prophage-like borders — zeroCountSearch","text":"List","code":""},{"path":"https://jlmaier12.github.io/TrIdent/news/index.html","id":"changes-in-0992","dir":"Changelog","previous_headings":"","what":"Changes in 0.99.2","title":"Changes in 0.99.2","text":"Updated vignette README BiocManager installation instructions Moved Acknowledgements, Funding, SessionInfo() ‘supplemental information’ section vignette Changed TOC_depth 2 3 vignette Updated formatting NEWS file Grouped related functions .R files easier troubleshooting Add verbose = TRUE/FALSE argument allow users choose whether print progress Added co-authors DESCRIPTION file Added additional logic input file validation Added better descriptions input file requirements main function .man pages Added rendered summary histogram plot output list Removed usage <<- Fixed improper usage lapply","code":""},{"path":"https://jlmaier12.github.io/TrIdent/news/index.html","id":"changes-in-0991","dir":"Changelog","previous_headings":"","what":"Changes in 0.99.1","title":"Changes in 0.99.1","text":"Fixed unit tests Bioc submission","code":""},{"path":"https://jlmaier12.github.io/TrIdent/news/index.html","id":"changes-in-0990","dir":"Changelog","previous_headings":"","what":"Changes in 0.99.0","title":"Changes in 0.99.0","text":"Bioc submission","code":""}]
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