From f39bb127202ae368aa845a7950987518a1ba8662 Mon Sep 17 00:00:00 2001
From: sigven <sigven@ifi.uio.no>
Date: Thu, 24 Oct 2024 09:25:49 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20sigven/p?=
 =?UTF-8?q?henOncoX@c529ace3c7bbc2b95ad4bfe927d6bdc1abf1c77b=20?=
 =?UTF-8?q?=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 404.html                    |  4 +-
 CODE_OF_CONDUCT.html        |  4 +-
 LICENSE-text.html           |  4 +-
 articles/index.html         |  4 +-
 articles/phenOncoX.html     | 76 ++++++++++++++++++-------------------
 authors.html                |  8 ++--
 index.html                  | 10 ++---
 pkgdown.js                  |  8 ++++
 pkgdown.yml                 |  4 +-
 reference/get_aux_maps.html |  4 +-
 reference/get_pox_data.html |  4 +-
 reference/get_terms.html    |  4 +-
 reference/get_tree.html     |  4 +-
 reference/index.html        |  4 +-
 reference/tidyeval.html     |  4 +-
 search.json                 |  2 +-
 16 files changed, 78 insertions(+), 70 deletions(-)

diff --git a/404.html b/404.html
index 0ecb194..e3bc9ed 100644
--- a/404.html
+++ b/404.html
@@ -27,7 +27,7 @@
 
     <a class="navbar-brand me-2" href="https://sigven.github.io/phenOncoX/index.html">phenOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.7.9</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.0</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">
@@ -67,7 +67,7 @@
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer>
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index 8055b84..65f8cca 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">phenOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.7.9</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.0</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">
@@ -108,7 +108,7 @@ <h2 id="attribution">Attribution<a class="anchor" aria-label="anchor" href="#att
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
diff --git a/LICENSE-text.html b/LICENSE-text.html
index 5778965..d7d9f34 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">phenOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.7.9</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.0</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">
@@ -62,7 +62,7 @@
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
diff --git a/articles/index.html b/articles/index.html
index e59a042..706fbb7 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">phenOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.7.9</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.0</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">
@@ -45,7 +45,7 @@ <h3>All vignettes</h3>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
diff --git a/articles/phenOncoX.html b/articles/phenOncoX.html
index 28af88c..31fdd14 100644
--- a/articles/phenOncoX.html
+++ b/articles/phenOncoX.html
@@ -26,7 +26,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">phenOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.7.9</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.0</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">
@@ -93,12 +93,12 @@ <h2 id="get-oncotree-terms">Get OncoTree terms<a class="anchor" aria-label="anch
 <span></span>
 <span><span class="va">oncotree</span> <span class="op">&lt;-</span> <span class="fu">phenOncoX</span><span class="fu">::</span><span class="fu"><a href="../reference/get_tree.html">get_tree</a></span><span class="op">(</span></span>
 <span>  cache_dir <span class="op">=</span> <span class="va">download_dir</span>, max_tree_depth <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-05 10:16:45] Downloading remote dataset from Google Drive to cache_dir</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-05 10:16:46] Reading from cache_dir = '/tmp/RtmpdWZcri', argument force_download = FALSE</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-05 10:16:46] Object 'oncotree_core' sucessfully loaded</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-05 10:16:46] md5 checksum is valid: 477b56fa8d39a647b190619ff3698021</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-05 10:16:46] Retrieved 797 records</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-05 10:16:46] Limiting OncoTree terms to those with a maximum tree depth of = '2'</span></span>
+<span><span class="co">#&gt; INFO  [2024-10-24 09:25:40] Downloading remote dataset from Google Drive to cache_dir</span></span>
+<span><span class="co">#&gt; INFO  [2024-10-24 09:25:42] Reading from cache_dir = '/tmp/Rtmpjnijth', argument force_download = FALSE</span></span>
+<span><span class="co">#&gt; INFO  [2024-10-24 09:25:42] Object 'oncotree_core' sucessfully loaded</span></span>
+<span><span class="co">#&gt; INFO  [2024-10-24 09:25:42] md5 checksum is valid: 0e1c05a3650ffb03d88f404843bcbb6a</span></span>
+<span><span class="co">#&gt; INFO  [2024-10-24 09:25:42] Retrieved 797 records</span></span>
+<span><span class="co">#&gt; INFO  [2024-10-24 09:25:42] Limiting OncoTree terms to those with a maximum tree depth of = '2'</span></span>
 <span></span>
 <span><span class="co">## Number of records</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/nrow.html" class="external-link">nrow</a></span><span class="op">(</span><span class="va">oncotree</span><span class="op">$</span><span class="va">records</span><span class="op">)</span></span>
@@ -126,15 +126,15 @@ <h3 id="get-all-oncotree-expanded-cancer-phenotype-terms">Get all (OncoTree-expa
 <span></span>
 <span><span class="va">oncoterms</span> <span class="op">&lt;-</span> <span class="fu">phenOncoX</span><span class="fu">::</span><span class="fu"><a href="../reference/get_terms.html">get_terms</a></span><span class="op">(</span></span>
 <span>  cache_dir <span class="op">=</span> <span class="va">download_dir</span><span class="op">)</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-05 10:16:46] Downloading remote dataset from Google Drive to cache_dir</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-05 10:16:49] Reading from cache_dir = '/tmp/RtmpdWZcri', argument force_download = FALSE</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-05 10:16:49] Object 'oncotree_expanded' sucessfully loaded</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-05 10:16:49] md5 checksum is valid: b2fb104bb66fd4b984f287aa7991928a</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-05 10:16:49] Retrieved 26095 records</span></span>
+<span><span class="co">#&gt; INFO  [2024-10-24 09:25:42] Downloading remote dataset from Google Drive to cache_dir</span></span>
+<span><span class="co">#&gt; INFO  [2024-10-24 09:25:45] Reading from cache_dir = '/tmp/Rtmpjnijth', argument force_download = FALSE</span></span>
+<span><span class="co">#&gt; INFO  [2024-10-24 09:25:45] Object 'oncotree_expanded' sucessfully loaded</span></span>
+<span><span class="co">#&gt; INFO  [2024-10-24 09:25:45] md5 checksum is valid: e1b920aed5d2daf4f13481f91d072481</span></span>
+<span><span class="co">#&gt; INFO  [2024-10-24 09:25:45] Retrieved 25377 records</span></span>
 <span></span>
 <span><span class="co">## Number of records</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/nrow.html" class="external-link">nrow</a></span><span class="op">(</span><span class="va">oncoterms</span><span class="op">$</span><span class="va">records</span><span class="op">)</span></span>
-<span><span class="co">#&gt; [1] 26095</span></span></code></pre></div>
+<span><span class="co">#&gt; [1] 25377</span></span></code></pre></div>
 <p><br><br></p>
 </div>
 <div class="section level3">
@@ -147,9 +147,9 @@ <h3 id="number-of-oncotree-expanded-cancer-phenotype-terms-per-primary-tumor-typ
 <span></span>
 <span><span class="va">oncoterms</span> <span class="op">&lt;-</span> <span class="fu">phenOncoX</span><span class="fu">::</span><span class="fu"><a href="../reference/get_terms.html">get_terms</a></span><span class="op">(</span></span>
 <span>  cache_dir <span class="op">=</span> <span class="va">download_dir</span><span class="op">)</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-05 10:16:49] Reading from cache_dir = '/tmp/RtmpdWZcri', argument force_download = FALSE</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-05 10:16:49] Object 'oncotree_expanded' sucessfully loaded</span></span>
-<span><span class="co">#&gt; INFO  [2024-09-05 10:16:49] Retrieved n = 26095 records</span></span>
+<span><span class="co">#&gt; INFO  [2024-10-24 09:25:45] Reading from cache_dir = '/tmp/Rtmpjnijth', argument force_download = FALSE</span></span>
+<span><span class="co">#&gt; INFO  [2024-10-24 09:25:45] Object 'oncotree_expanded' sucessfully loaded</span></span>
+<span><span class="co">#&gt; INFO  [2024-10-24 09:25:45] Retrieved n = 25377 records</span></span>
 <span></span>
 <span><span class="co">## Number of records</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/as.data.frame.html" class="external-link">as.data.frame</a></span><span class="op">(</span><span class="va">oncoterms</span><span class="op">$</span><span class="va">records</span> <span class="op">|&gt;</span></span>
@@ -159,26 +159,26 @@ <h3 id="number-of-oncotree-expanded-cancer-phenotype-terms-per-primary-tumor-typ
 <span>                   .groups <span class="op">=</span> <span class="st">"drop"</span><span class="op">)</span> <span class="op">|&gt;</span></span>
 <span>  <span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="fu">dplyr</span><span class="fu">::</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/desc.html" class="external-link">desc</a></span><span class="op">(</span><span class="va">num_terms</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="co">#&gt;                 primary_site num_terms</span></span>
-<span><span class="co">#&gt; 1                   Lymphoid      4040</span></span>
-<span><span class="co">#&gt; 2                Soft Tissue      2826</span></span>
-<span><span class="co">#&gt; 3                  CNS/Brain      2293</span></span>
+<span><span class="co">#&gt; 1                   Lymphoid      4037</span></span>
+<span><span class="co">#&gt; 2                Soft Tissue      2828</span></span>
+<span><span class="co">#&gt; 3                  CNS/Brain      2294</span></span>
 <span><span class="co">#&gt; 4              Head and Neck      2273</span></span>
-<span><span class="co">#&gt; 5                       Skin      2074</span></span>
-<span><span class="co">#&gt; 6                    Myeloid      1776</span></span>
-<span><span class="co">#&gt; 7          Esophagus/Stomach      1170</span></span>
-<span><span class="co">#&gt; 8                       Lung      1086</span></span>
-<span><span class="co">#&gt; 9               Colon/Rectum       966</span></span>
-<span><span class="co">#&gt; 10      Ovary/Fallopian Tube       851</span></span>
-<span><span class="co">#&gt; 11                    Breast       781</span></span>
-<span><span class="co">#&gt; 12                      Bone       557</span></span>
-<span><span class="co">#&gt; 13     Bladder/Urinary Tract       484</span></span>
+<span><span class="co">#&gt; 5                       Skin      1817</span></span>
+<span><span class="co">#&gt; 6                    Myeloid      1777</span></span>
+<span><span class="co">#&gt; 7                       Lung      1086</span></span>
+<span><span class="co">#&gt; 8               Colon/Rectum       966</span></span>
+<span><span class="co">#&gt; 9       Ovary/Fallopian Tube       851</span></span>
+<span><span class="co">#&gt; 10                    Breast       781</span></span>
+<span><span class="co">#&gt; 11         Esophagus/Stomach       719</span></span>
+<span><span class="co">#&gt; 12                      Bone       551</span></span>
+<span><span class="co">#&gt; 13     Bladder/Urinary Tract       482</span></span>
 <span><span class="co">#&gt; 14                    Uterus       451</span></span>
 <span><span class="co">#&gt; 15             Biliary Tract       416</span></span>
 <span><span class="co">#&gt; 16                     Liver       415</span></span>
-<span><span class="co">#&gt; 17                    Kidney       397</span></span>
+<span><span class="co">#&gt; 17                    Kidney       396</span></span>
 <span><span class="co">#&gt; 18                  Pancreas       343</span></span>
 <span><span class="co">#&gt; 19 Peripheral Nervous System       292</span></span>
-<span><span class="co">#&gt; 20                    Cervix       288</span></span>
+<span><span class="co">#&gt; 20                    Cervix       287</span></span>
 <span><span class="co">#&gt; 21                       Eye       274</span></span>
 <span><span class="co">#&gt; 22              Vulva/Vagina       265</span></span>
 <span><span class="co">#&gt; 23                   Thyroid       250</span></span>
@@ -229,7 +229,7 @@ <h2 id="session-info">Session Info<a class="anchor" aria-label="anchor" href="#s
 <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 4.4.1 (2024-06-14)</span></span>
 <span><span class="co">#&gt; Platform: x86_64-pc-linux-gnu</span></span>
-<span><span class="co">#&gt; Running under: Ubuntu 22.04.4 LTS</span></span>
+<span><span class="co">#&gt; Running under: Ubuntu 22.04.5 LTS</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; Matrix products: default</span></span>
 <span><span class="co">#&gt; BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 </span></span>
@@ -248,16 +248,16 @@ <h2 id="session-info">Session Info<a class="anchor" aria-label="anchor" href="#s
 <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; loaded via a namespace (and not attached):</span></span>
-<span><span class="co">#&gt;  [1] jsonlite_1.8.8    dplyr_1.1.4       compiler_4.4.1    crayon_1.5.3     </span></span>
-<span><span class="co">#&gt;  [5] tidyselect_1.2.1  phenOncoX_0.7.9   jquerylib_0.1.4   systemfonts_1.1.0</span></span>
+<span><span class="co">#&gt;  [1] jsonlite_1.8.9    dplyr_1.1.4       compiler_4.4.1    crayon_1.5.3     </span></span>
+<span><span class="co">#&gt;  [5] tidyselect_1.2.1  phenOncoX_0.8.0   jquerylib_0.1.4   systemfonts_1.1.0</span></span>
 <span><span class="co">#&gt;  [9] textshaping_0.4.0 yaml_2.3.10       fastmap_1.2.0     R6_2.5.1         </span></span>
-<span><span class="co">#&gt; [13] generics_0.1.3    curl_5.2.2        knitr_1.48        htmlwidgets_1.6.4</span></span>
+<span><span class="co">#&gt; [13] generics_0.1.3    curl_5.2.3        knitr_1.48        htmlwidgets_1.6.4</span></span>
 <span><span class="co">#&gt; [17] tibble_3.2.1      desc_1.4.3        bslib_0.8.0       pillar_1.9.0     </span></span>
 <span><span class="co">#&gt; [21] rlang_1.1.4       DT_0.33           utf8_1.2.4        cachem_1.1.0     </span></span>
-<span><span class="co">#&gt; [25] lgr_0.4.4         xfun_0.47         fs_1.6.4          sass_0.4.9       </span></span>
-<span><span class="co">#&gt; [29] cli_3.6.3         withr_3.0.1       pkgdown_2.1.0     magrittr_2.0.3   </span></span>
+<span><span class="co">#&gt; [25] lgr_0.4.4         xfun_0.48         fs_1.6.4          sass_0.4.9       </span></span>
+<span><span class="co">#&gt; [29] cli_3.6.3         withr_3.0.1       pkgdown_2.1.1     magrittr_2.0.3   </span></span>
 <span><span class="co">#&gt; [33] crosstalk_1.2.1   digest_0.6.37     lifecycle_1.0.4   vctrs_0.6.5      </span></span>
-<span><span class="co">#&gt; [37] evaluate_0.24.0   gargle_1.5.2      glue_1.7.0        ragg_1.3.2       </span></span>
+<span><span class="co">#&gt; [37] evaluate_1.0.1    gargle_1.5.2      glue_1.8.0        ragg_1.3.3       </span></span>
 <span><span class="co">#&gt; [41] googledrive_2.1.1 fansi_1.0.6       httr_1.4.7        rmarkdown_2.28   </span></span>
 <span><span class="co">#&gt; [45] purrr_1.0.2       tools_4.4.1       pkgconfig_2.0.3   htmltools_0.5.8.1</span></span></code></pre></div>
 <p><br><br></p>
@@ -310,7 +310,7 @@ <h2 class="unnumbered" id="references">References<a class="anchor" aria-label="a
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer>
diff --git a/authors.html b/authors.html
index 229b07b..46abfad 100644
--- a/authors.html
+++ b/authors.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">phenOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.7.9</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.0</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">
@@ -45,13 +45,13 @@ <h2 id="citation">Citation</h2>
 
       <p>Nakken S (2024).
 <em>phenOncoX: A phenotype ontology map for cancer</em>.
-R package version 0.7.9, <a href="https://sigven.github.io/phenOncoX">https://sigven.github.io/phenOncoX</a>.
+R package version 0.8.0, <a href="https://sigven.github.io/phenOncoX">https://sigven.github.io/phenOncoX</a>.
 </p>
       <pre>@Manual{,
   title = {phenOncoX: A phenotype ontology map for cancer},
   author = {Sigve Nakken},
   year = {2024},
-  note = {R package version 0.7.9},
+  note = {R package version 0.8.0},
   url = {https://sigven.github.io/phenOncoX},
 }</pre>
     </div>
@@ -65,7 +65,7 @@ <h2 id="citation">Citation</h2>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
diff --git a/index.html b/index.html
index 4abc93b..14e40fc 100644
--- a/index.html
+++ b/index.html
@@ -29,7 +29,7 @@
 
     <a class="navbar-brand me-2" href="index.html">phenOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.7.9</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.0</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">
@@ -71,11 +71,11 @@
 <p><strong>phenOncoX</strong> is an R data package that attempts to address this challenge. In short, <strong>phenOncoX</strong> provides a global cross-mapped set of phenotype ontology terms attributed to cancer phenotypes.</p>
 <p>The mapping established within <strong>phenOncoX</strong> is semi-manually curated, using <a href="http://oncotree.mskcc.org/#/home" class="external-link">OncoTree</a> as the starting point for a list of <a href="https://www.ncbi.nlm.nih.gov/medgen/" class="external-link">UMLS</a> phenotype terms per cancer subtype/primary site. Next, <strong>phenOncoX</strong> appends a number of phenotypes attributed to heritable cancer conditions. Furthermore, each cancer subtype entry in <em>OncoTree</em> is expanded with additional subtypes that are found in the <em>UMLS</em> child-parent hierarchy of disease terms.</p>
 <p>For each entry in the final list of phenotype terms, we make cross-mappings with phenotype terms from <a href="https://github.com/EBISPOT/efo" class="external-link">EFO</a>, <a href="https://disease-ontology.org/" class="external-link">DO</a>, and the <a href="https://www.who.int/standards/classifications/classification-of-diseases" class="external-link">ICD10 classification</a>.</p>
-<p>As of early September 2024, the following ontology versions are used to create the mapping:</p>
+<p>As of late October 2024, the following ontology versions are used to create the mapping:</p>
 <ul>
 <li>OncoTree (2021_11_02)</li>
-<li>Experimental Factor Ontology v3.69.0 (2024-08-15)</li>
-<li>Disease Ontology (v2024-08-28)</li>
+<li>Experimental Factor Ontology v3.71.0 (2024-10-15)</li>
+<li>Disease Ontology (v2024-09-27)</li>
 </ul>
 <p>The package offers a few pre-processed datasets, along with metadata, that the user can retrieve and use for their own projects or set-ups. The package utilizes the <a href="https://googledrive.tidyverse.org/" class="external-link">googledrive</a> R package to download the pre-processed and documented datasets to a local cache directory provided by the user.</p>
 <p><strong>IMPORTANT NOTE</strong>: The mapping established by <strong>phenOncoX</strong> attempts to be comprehensive, but we acknowledge that the presence of missing or erroneous cross-references might still occur.</p>
@@ -149,7 +149,7 @@ <h2 data-toc-skip>Developers</h2>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer>
diff --git a/pkgdown.js b/pkgdown.js
index 9757bf9..1a99c65 100644
--- a/pkgdown.js
+++ b/pkgdown.js
@@ -152,3 +152,11 @@ async function searchFuse(query, callback) {
   });
   });
 })(window.jQuery || window.$)
+
+document.addEventListener('keydown', function(event) {
+  // Check if the pressed key is '/'
+  if (event.key === '/') {
+    event.preventDefault();  // Prevent any default action associated with the '/' key
+    document.getElementById('search-input').focus();  // Set focus to the search input
+  }
+});
diff --git a/pkgdown.yml b/pkgdown.yml
index 9d23149..aadb77b 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,9 +1,9 @@
 pandoc: 3.1.11
-pkgdown: 2.1.0
+pkgdown: 2.1.1
 pkgdown_sha: ~
 articles:
   phenOncoX: phenOncoX.html
-last_built: 2024-09-05T10:16Z
+last_built: 2024-10-24T09:25Z
 urls:
   reference: https://sigven.github.io/phenOncoX/reference
   article: https://sigven.github.io/phenOncoX/articles
diff --git a/reference/get_aux_maps.html b/reference/get_aux_maps.html
index 9092f74..d97ed3e 100644
--- a/reference/get_aux_maps.html
+++ b/reference/get_aux_maps.html
@@ -21,7 +21,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">phenOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.7.9</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.0</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">
@@ -106,7 +106,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
diff --git a/reference/get_pox_data.html b/reference/get_pox_data.html
index f7b698e..eef696b 100644
--- a/reference/get_pox_data.html
+++ b/reference/get_pox_data.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">phenOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.7.9</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.0</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">
@@ -73,7 +73,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
diff --git a/reference/get_terms.html b/reference/get_terms.html
index a8675c3..a56c02f 100644
--- a/reference/get_terms.html
+++ b/reference/get_terms.html
@@ -27,7 +27,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">phenOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.7.9</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.0</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">
@@ -151,7 +151,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
diff --git a/reference/get_tree.html b/reference/get_tree.html
index 4a548b2..a899640 100644
--- a/reference/get_tree.html
+++ b/reference/get_tree.html
@@ -19,7 +19,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">phenOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.7.9</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.0</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">
@@ -138,7 +138,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
diff --git a/reference/index.html b/reference/index.html
index 770f68e..7e3af33 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">phenOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.7.9</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.0</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">
@@ -68,7 +68,7 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
diff --git a/reference/tidyeval.html b/reference/tidyeval.html
index 328b3d9..ec4d60d 100644
--- a/reference/tidyeval.html
+++ b/reference/tidyeval.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">phenOncoX</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.7.9</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.8.0</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">
@@ -46,7 +46,7 @@
 </div>
 
 <div class="pkgdown-footer-right">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.0.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
 </div>
 
     </footer></div>
diff --git a/search.json b/search.json
index b3a8a3c..c528f97 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":[]},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement [INSERT CONTACT METHOD]. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.0, available https://www.contributor-covenant.org/version/2/0/ code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https:// www.contributor-covenant.org/translations.","code":""},{"path":"https://sigven.github.io/phenOncoX/articles/phenOncoX.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"Getting started","text":"","code":"if (!(\"remotes\" %in% installed.packages()) {   install.packages(\"remotes\") } remotes::install_github('sigven/phenOncoX')"},{"path":"https://sigven.github.io/phenOncoX/articles/phenOncoX.html","id":"get-oncotree-terms","dir":"Articles","previous_headings":"","what":"Get OncoTree terms","title":"Getting started","text":"shows retrieve cancer phenotype terms , defined OncoTree (max tree depth = 2)","code":"## load the data download_dir <- tempdir()  oncotree <- phenOncoX::get_tree(   cache_dir = download_dir, max_tree_depth = 2) #> INFO  [2024-09-05 10:16:45] Downloading remote dataset from Google Drive to cache_dir #> INFO  [2024-09-05 10:16:46] Reading from cache_dir = '/tmp/RtmpdWZcri', argument force_download = FALSE #> INFO  [2024-09-05 10:16:46] Object 'oncotree_core' sucessfully loaded #> INFO  [2024-09-05 10:16:46] md5 checksum is valid: 477b56fa8d39a647b190619ff3698021 #> INFO  [2024-09-05 10:16:46] Retrieved 797 records #> INFO  [2024-09-05 10:16:46] Limiting OncoTree terms to those with a maximum tree depth of = '2'  ## Number of records nrow(oncotree$records) #> [1] 251  ## Show metadata for underlying resources oncotree$metadata #>     source                                    source_description #> 1 OncoTree A cancer classification system for precision oncology #>                         source_url #> 1 http://oncotree.mskcc.org/#/home #>                                         source_citation source_version #> 1 Kundra et al., JCO Clin Cancer Inform, 2021; 33625877     2021_11_02 #>   source_abbreviation source_license #> 1            oncotree      CC BY 4.0 #>                             source_license_url #> 1 https://creativecommons.org/licenses/by/4.0/"},{"path":"https://sigven.github.io/phenOncoX/articles/phenOncoX.html","id":"get-all-oncotree-expanded-cancer-phenotype-terms","dir":"Articles","previous_headings":"Get OncoTree terms","what":"Get all (OncoTree-expanded) cancer phenotype terms","title":"Getting started","text":"","code":"## get all cancer phenotype terms  oncoterms <- phenOncoX::get_terms(   cache_dir = download_dir) #> INFO  [2024-09-05 10:16:46] Downloading remote dataset from Google Drive to cache_dir #> INFO  [2024-09-05 10:16:49] Reading from cache_dir = '/tmp/RtmpdWZcri', argument force_download = FALSE #> INFO  [2024-09-05 10:16:49] Object 'oncotree_expanded' sucessfully loaded #> INFO  [2024-09-05 10:16:49] md5 checksum is valid: b2fb104bb66fd4b984f287aa7991928a #> INFO  [2024-09-05 10:16:49] Retrieved 26095 records  ## Number of records nrow(oncoterms$records) #> [1] 26095"},{"path":"https://sigven.github.io/phenOncoX/articles/phenOncoX.html","id":"number-of-oncotree-expanded-cancer-phenotype-terms-per-primary-tumor-typetissue","dir":"Articles","previous_headings":"Get OncoTree terms","what":"Number of (OncoTree-expanded) cancer phenotype terms per primary tumor type/tissue","title":"Getting started","text":"","code":"## get all cancer phenotype terms  oncoterms <- phenOncoX::get_terms(   cache_dir = download_dir) #> INFO  [2024-09-05 10:16:49] Reading from cache_dir = '/tmp/RtmpdWZcri', argument force_download = FALSE #> INFO  [2024-09-05 10:16:49] Object 'oncotree_expanded' sucessfully loaded #> INFO  [2024-09-05 10:16:49] Retrieved n = 26095 records  ## Number of records as.data.frame(oncoterms$records |>   dplyr::filter(!is.na(primary_site)) |>   dplyr::group_by(primary_site) |>    dplyr::summarise(num_terms = dplyr::n(),                    .groups = \"drop\") |>   dplyr::arrange(dplyr::desc(num_terms))) #>                 primary_site num_terms #> 1                   Lymphoid      4040 #> 2                Soft Tissue      2826 #> 3                  CNS/Brain      2293 #> 4              Head and Neck      2273 #> 5                       Skin      2074 #> 6                    Myeloid      1776 #> 7          Esophagus/Stomach      1170 #> 8                       Lung      1086 #> 9               Colon/Rectum       966 #> 10      Ovary/Fallopian Tube       851 #> 11                    Breast       781 #> 12                      Bone       557 #> 13     Bladder/Urinary Tract       484 #> 14                    Uterus       451 #> 15             Biliary Tract       416 #> 16                     Liver       415 #> 17                    Kidney       397 #> 18                  Pancreas       343 #> 19 Peripheral Nervous System       292 #> 20                    Cervix       288 #> 21                       Eye       274 #> 22              Vulva/Vagina       265 #> 23                   Thyroid       250 #> 24                    Testis       239 #> 25                  Prostate       207 #> 26             Other/Unknown       176 #> 27                    Pleura       124 #> 28                Peritoneum        99 #> 29                    Thymus        87 #> 30             Adrenal Gland        70 #> 31                     Penis        61 #> 32          Ampulla of Vater        46"},{"path":"https://sigven.github.io/phenOncoX/articles/phenOncoX.html","id":"get-all-oncotree-expanded-cancer-phenotype-terms-relevant-for-prostate-cancer","dir":"Articles","previous_headings":"Get OncoTree terms","what":"Get all (OncoTree-expanded) cancer phenotype terms relevant for prostate cancer","title":"Getting started","text":"","code":"## get all oncoterms for prostate cancer oncoterms_prostate <- phenOncoX::get_terms(   cache_dir = download_dir,    site = \"Prostate\")  ## Make as datatable prostate_terms_table <- DT::datatable(   dplyr::select(     oncoterms_prostate$records,      primary_site, cui, cui_name,     dplyr::everything()),   escape = FALSE,   extensions = c(\"Buttons\", \"Responsive\"),    width = \"100%\",   options = list(     buttons = c(\"csv\", \"excel\"),      dom = \"Bfrtip\"))"},{"path":"https://sigven.github.io/phenOncoX/articles/phenOncoX.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session Info","title":"Getting started","text":"","code":"# set eval = FALSE if you don't want this info (useful for reproducibility)  # to appear sessionInfo() #> R version 4.4.1 (2024-06-14) #> Platform: x86_64-pc-linux-gnu #> Running under: Ubuntu 22.04.4 LTS #>  #> Matrix products: default #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 #>  #> locale: #>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        #>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8    #>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C           #> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C    #>  #> time zone: UTC #> tzcode source: system (glibc) #>  #> attached base packages: #> [1] stats     graphics  grDevices utils     datasets  methods   base      #>  #> loaded via a namespace (and not attached): #>  [1] jsonlite_1.8.8    dplyr_1.1.4       compiler_4.4.1    crayon_1.5.3      #>  [5] tidyselect_1.2.1  phenOncoX_0.7.9   jquerylib_0.1.4   systemfonts_1.1.0 #>  [9] textshaping_0.4.0 yaml_2.3.10       fastmap_1.2.0     R6_2.5.1          #> [13] generics_0.1.3    curl_5.2.2        knitr_1.48        htmlwidgets_1.6.4 #> [17] tibble_3.2.1      desc_1.4.3        bslib_0.8.0       pillar_1.9.0      #> [21] rlang_1.1.4       DT_0.33           utf8_1.2.4        cachem_1.1.0      #> [25] lgr_0.4.4         xfun_0.47         fs_1.6.4          sass_0.4.9        #> [29] cli_3.6.3         withr_3.0.1       pkgdown_2.1.0     magrittr_2.0.3    #> [33] crosstalk_1.2.1   digest_0.6.37     lifecycle_1.0.4   vctrs_0.6.5       #> [37] evaluate_0.24.0   gargle_1.5.2      glue_1.7.0        ragg_1.3.2        #> [41] googledrive_2.1.1 fansi_1.0.6       httr_1.4.7        rmarkdown_2.28    #> [45] purrr_1.0.2       tools_4.4.1       pkgconfig_2.0.3   htmltools_0.5.8.1"},{"path":[]},{"path":"https://sigven.github.io/phenOncoX/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Sigve Nakken. Author, maintainer.","code":""},{"path":"https://sigven.github.io/phenOncoX/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Nakken S (2024). phenOncoX: phenotype ontology map cancer. R package version 0.7.9, https://sigven.github.io/phenOncoX.","code":"@Manual{,   title = {phenOncoX: A phenotype ontology map for cancer},   author = {Sigve Nakken},   year = {2024},   note = {R package version 0.7.9},   url = {https://sigven.github.io/phenOncoX}, }"},{"path":"https://sigven.github.io/phenOncoX/index.html","id":"phenoncox-","dir":"","previous_headings":"","what":"A phenotype ontology map for cancer","title":"A phenotype ontology map for cancer","text":"ontological definition disease enables type disease singularly classified formalized structure. intention, use disease ontology terms facilitate cross-link information separate disease-related knowledge resources given domain. However, multiple disease ontology frameworks developed human disease (.e. OncoTree, Experimental Factor Ontology (EFO), Disease Ontology (), UMLS, ICD-10), used different extents across knowledge resources oncology domain, following: gene-disease associations drug-disease indications variant-disease associations order integrate knowledge resources, henceforth need cross-link map entries across disease ontologies extent possible. phenOncoX R data package attempts address challenge. short, phenOncoX provides global cross-mapped set phenotype ontology terms attributed cancer phenotypes. mapping established within phenOncoX semi-manually curated, using OncoTree starting point list UMLS phenotype terms per cancer subtype/primary site. Next, phenOncoX appends number phenotypes attributed heritable cancer conditions. Furthermore, cancer subtype entry OncoTree expanded additional subtypes found UMLS child-parent hierarchy disease terms. entry final list phenotype terms, make cross-mappings phenotype terms EFO, , ICD10 classification. early September 2024, following ontology versions used create mapping: OncoTree (2021_11_02) Experimental Factor Ontology v3.69.0 (2024-08-15) Disease Ontology (v2024-08-28) package offers pre-processed datasets, along metadata, user can retrieve use projects set-ups. package utilizes googledrive R package download pre-processed documented datasets local cache directory provided user. IMPORTANT NOTE: mapping established phenOncoX attempts comprehensive, acknowledge presence missing erroneous cross-references might still occur.","code":""},{"path":"https://sigven.github.io/phenOncoX/index.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting started","title":"A phenotype ontology map for cancer","text":"Installation instructions Usage examples","code":""},{"path":"https://sigven.github.io/phenOncoX/index.html","id":"contact","dir":"","previous_headings":"","what":"Contact","title":"A phenotype ontology map for cancer","text":"sigven ifi.uio.","code":""},{"path":"https://sigven.github.io/phenOncoX/index.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"A phenotype ontology map for cancer","text":"Please note project released Contributor Code Conduct. participating project agree abide terms.","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_aux_maps.html","id":null,"dir":"Reference","previous_headings":"","what":"Get auxiliary phenotype ontology maps — get_aux_maps","title":"Get auxiliary phenotype ontology maps — get_aux_maps","text":"Downloads returns multiple phenotype dictionaries used cross-referencing terms, including UMLS, EFO, , ICD10. dataset comes list object, two elements: metadata - data frame metadata regarding annotation resources used records - list object multiple lists/data.frames","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_aux_maps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get auxiliary phenotype ontology maps — get_aux_maps","text":"","code":"get_aux_maps(cache_dir = NA, force_download = FALSE)"},{"path":"https://sigven.github.io/phenOncoX/reference/get_aux_maps.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get auxiliary phenotype ontology maps — get_aux_maps","text":"cache_dir Local directory data download force_download Logical indicating local cache overwritten (set TRUE re-download file exists cache)","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_aux_maps.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get auxiliary phenotype ontology maps — get_aux_maps","text":"metadata - data frame 4 rows 6 columns: source - gene annotation source annotation_data - type annotations used url - URL annotation resource citation - publication cite annotation source (citation; PMID) version - version used abbreviation - abbreviation used column names records records - list following elements: umls - List UMLS data dictionaries - Data frame identifiers/names efo - List EFO data dictionaries icd10 - Data frame CUI ICD10 cross-reference","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_aux_maps.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get auxiliary phenotype ontology maps — get_aux_maps","text":"","code":"if (FALSE) { # \\dontrun{ library(phenOncoX) oncology_terms <- get_aux_maps(cache_dir = tempdir()) } # }"},{"path":"https://sigven.github.io/phenOncoX/reference/get_pox_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Function that retrieves phenOncoX data from Google Drive/local cache — get_pox_data","title":"Function that retrieves phenOncoX data from Google Drive/local cache — get_pox_data","text":"Function retrieves phenOncoX data Google Drive/local cache","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_pox_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function that retrieves phenOncoX data from Google Drive/local cache — get_pox_data","text":"","code":"get_pox_data(cache_dir = NA, force_download = FALSE, db = \"oncotree_core\")"},{"path":"https://sigven.github.io/phenOncoX/reference/get_pox_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function that retrieves phenOncoX data from Google Drive/local cache — get_pox_data","text":"cache_dir Local directory data download force_download Logical indicating local cache overwritten (set TRUE re-download file exists cache) db type dataset retrieved","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_pox_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function that retrieves phenOncoX data from Google Drive/local cache — get_pox_data","text":"pre-processed ontology terms records/metadata auxiliary maps","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_terms.html","id":null,"dir":"Reference","previous_headings":"","what":"Get oncology-relevant phenotype terms — get_terms","title":"Get oncology-relevant phenotype terms — get_terms","text":"Downloads returns dataset expanded set oncology-relevant phenotype terms (UMLS), using OncoTree starting point. expansion conducted tracking MeSH/UMLS tree structure phenotype terms. record comes cross-references Disease Ontology (), Experimental Factor Ontology (EFO), ICD10 wherever available. dataset comes list object, two elements: metadata - data frame metadata regarding annotation resources used records - data frame phenotype terms","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_terms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get oncology-relevant phenotype terms — get_terms","text":"","code":"get_terms(   cache_dir = NA,   force_download = FALSE,   site = NA,   ignore_minor_type = FALSE )"},{"path":"https://sigven.github.io/phenOncoX/reference/get_terms.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get oncology-relevant phenotype terms — get_terms","text":"cache_dir Local directory data download force_download Logical indicating local cache overwritten (set TRUE re-download file exists cache) site limit phenotype terms relevant given primary tumor type/site. Possible values: 'Adrenal Gland', 'Ampulla Vater', 'Biliary Tract', 'Bladder/Urinary Tract', 'Bone', 'Breast', 'Cervix', 'CNS/Brain', 'Colon/Rectum', 'Esophagus/Stomach', 'Eye', 'Head Neck', 'Kidney', 'Liver', 'Lung', 'Lymphoid', 'Myeloid', '/Unknown', 'Ovary/Fallopian Tube', 'Pancreas', 'Penis', 'Peripheral Nervous System', 'Peritoneum', 'Pleura', 'Prostate', 'Skin', 'Soft Tissue', 'Testis', 'Thymus', 'Thyroid', 'Uterus', 'Vulva/Vagina' ignore_minor_type logical indicating minor tumor types excluded ","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_terms.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get oncology-relevant phenotype terms — get_terms","text":"metadata - data frame 5 rows 6 columns: source - gene annotation source annotation_data - type annotations used url - URL annotation resource citation - publication cite annotation source (citation; PMID) version - version used abbreviation - abbreviation used column names records records - data frame following columns: primary_site - Primary tumor type/site ot_main_type - Main tumor type (OncoTree) ot_name - Phenotype name (OncoTree) ot_level - Tree level (OncoTree) ot_code - Phenotype code (OncoTree) ot_code_path - Tree code path (OncoTree) cui - Concept unique identifier (UMLS) cui_name - Phenotype name (UMLS) efo_id - EFO identifier efo_name - EFO name do_id - identifier do_name - name do_cancer_slim - identifier part cancer slim dictionary (TRUE/FALSE) minor_type - logical indicating whether term part minor tumor type/site icd10_code - ICD10 identifier source - term indicating dataset source","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_terms.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get oncology-relevant phenotype terms — get_terms","text":"","code":"if (FALSE) { # \\dontrun{ library(phenOncoX) oncology_terms <- get_terms(cache_dir = tempdir()) } # }"},{"path":"https://sigven.github.io/phenOncoX/reference/get_tree.html","id":null,"dir":"Reference","previous_headings":"","what":"Get core phenotype terms from OncoTree — get_tree","title":"Get core phenotype terms from OncoTree — get_tree","text":"Downloads returns dataset curated phenotype terms (UMLS) OncoTree. dataset comes list object, two elements: metadata - data frame metadata regarding annotation resources used records - data frame phenotype terms","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_tree.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get core phenotype terms from OncoTree — get_tree","text":"","code":"get_tree(   cache_dir = NA,   force_download = FALSE,   site = NA,   max_tree_depth = 6,   ignore_minor_type = FALSE )"},{"path":"https://sigven.github.io/phenOncoX/reference/get_tree.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get core phenotype terms from OncoTree — get_tree","text":"cache_dir Local directory data download force_download Logical indicating local cache overwritten (set TRUE re-download file exists cache) site limit OncoTree terms relevant given primary tumor type/site. Possible values: 'Adrenal Gland', 'Ampulla Vater', 'Biliary Tract', 'Bladder/Urinary Tract', 'Bone', 'Breast', 'Cervix', 'CNS/Brain', 'Colon/Rectum', 'Esophagus/Stomach', 'Eye', 'Head Neck', 'Kidney', 'Liver', 'Lung', 'Lymphoid', 'Myeloid', '/Unknown', 'Ovary/Fallopian Tube', 'Pancreas', 'Penis', 'Peripheral Nervous System', 'Peritoneum', 'Pleura', 'Prostate', 'Skin', 'Soft Tissue', 'Testis', 'Thymus', 'Thyroid', 'Uterus', 'Vulva/Vagina' max_tree_depth consider terms given depth OncoTree (integer 1-6, default: 6) ignore_minor_type logical indicating minor tumor types excluded ","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_tree.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get core phenotype terms from OncoTree — get_tree","text":"metadata - data frame 1 row 6 columns: source - gene annotation source annotation_data - type annotations used url - URL annotation resource citation - publication cite annotation source (citation; PMID) version - version used abbreviation - abbreviation used column names records records - data frame following columns: primary_site - Primary tumor type/site ot_main_type - Main tumor type (OncoTree) ot_name - Phenotype name (OncoTree) ot_level - Tree level (OncoTree) ot_code - Phenotype code (OncoTree) ot_code_path - Tree code path (OncoTree) cui - Concept unique identifier (UMLS) cui_name - Phenotype name (UMLS) minor_type - logical indicating whether term part minor tumor type/site source - term indicating dataset source","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_tree.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get core phenotype terms from OncoTree — get_tree","text":"","code":"if (FALSE) { # \\dontrun{ library(phenOncoX) oncology_terms <- get_tree(cache_dir = tempdir()) } # }"},{"path":"https://sigven.github.io/phenOncoX/reference/tidyeval.html","id":null,"dir":"Reference","previous_headings":"","what":"Tidy eval helpers — tidyeval","title":"Tidy eval helpers — tidyeval","text":"https://cran.r-project.org/web/packages/dplyr/vignettes/programming.html","code":""}]
+[{"path":[]},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement [INSERT CONTACT METHOD]. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://sigven.github.io/phenOncoX/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.0, available https://www.contributor-covenant.org/version/2/0/ code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https:// www.contributor-covenant.org/translations.","code":""},{"path":"https://sigven.github.io/phenOncoX/articles/phenOncoX.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"Getting started","text":"","code":"if (!(\"remotes\" %in% installed.packages()) {   install.packages(\"remotes\") } remotes::install_github('sigven/phenOncoX')"},{"path":"https://sigven.github.io/phenOncoX/articles/phenOncoX.html","id":"get-oncotree-terms","dir":"Articles","previous_headings":"","what":"Get OncoTree terms","title":"Getting started","text":"shows retrieve cancer phenotype terms , defined OncoTree (max tree depth = 2)","code":"## load the data download_dir <- tempdir()  oncotree <- phenOncoX::get_tree(   cache_dir = download_dir, max_tree_depth = 2) #> INFO  [2024-10-24 09:25:40] Downloading remote dataset from Google Drive to cache_dir #> INFO  [2024-10-24 09:25:42] Reading from cache_dir = '/tmp/Rtmpjnijth', argument force_download = FALSE #> INFO  [2024-10-24 09:25:42] Object 'oncotree_core' sucessfully loaded #> INFO  [2024-10-24 09:25:42] md5 checksum is valid: 0e1c05a3650ffb03d88f404843bcbb6a #> INFO  [2024-10-24 09:25:42] Retrieved 797 records #> INFO  [2024-10-24 09:25:42] Limiting OncoTree terms to those with a maximum tree depth of = '2'  ## Number of records nrow(oncotree$records) #> [1] 251  ## Show metadata for underlying resources oncotree$metadata #>     source                                    source_description #> 1 OncoTree A cancer classification system for precision oncology #>                         source_url #> 1 http://oncotree.mskcc.org/#/home #>                                         source_citation source_version #> 1 Kundra et al., JCO Clin Cancer Inform, 2021; 33625877     2021_11_02 #>   source_abbreviation source_license #> 1            oncotree      CC BY 4.0 #>                             source_license_url #> 1 https://creativecommons.org/licenses/by/4.0/"},{"path":"https://sigven.github.io/phenOncoX/articles/phenOncoX.html","id":"get-all-oncotree-expanded-cancer-phenotype-terms","dir":"Articles","previous_headings":"Get OncoTree terms","what":"Get all (OncoTree-expanded) cancer phenotype terms","title":"Getting started","text":"","code":"## get all cancer phenotype terms  oncoterms <- phenOncoX::get_terms(   cache_dir = download_dir) #> INFO  [2024-10-24 09:25:42] Downloading remote dataset from Google Drive to cache_dir #> INFO  [2024-10-24 09:25:45] Reading from cache_dir = '/tmp/Rtmpjnijth', argument force_download = FALSE #> INFO  [2024-10-24 09:25:45] Object 'oncotree_expanded' sucessfully loaded #> INFO  [2024-10-24 09:25:45] md5 checksum is valid: e1b920aed5d2daf4f13481f91d072481 #> INFO  [2024-10-24 09:25:45] Retrieved 25377 records  ## Number of records nrow(oncoterms$records) #> [1] 25377"},{"path":"https://sigven.github.io/phenOncoX/articles/phenOncoX.html","id":"number-of-oncotree-expanded-cancer-phenotype-terms-per-primary-tumor-typetissue","dir":"Articles","previous_headings":"Get OncoTree terms","what":"Number of (OncoTree-expanded) cancer phenotype terms per primary tumor type/tissue","title":"Getting started","text":"","code":"## get all cancer phenotype terms  oncoterms <- phenOncoX::get_terms(   cache_dir = download_dir) #> INFO  [2024-10-24 09:25:45] Reading from cache_dir = '/tmp/Rtmpjnijth', argument force_download = FALSE #> INFO  [2024-10-24 09:25:45] Object 'oncotree_expanded' sucessfully loaded #> INFO  [2024-10-24 09:25:45] Retrieved n = 25377 records  ## Number of records as.data.frame(oncoterms$records |>   dplyr::filter(!is.na(primary_site)) |>   dplyr::group_by(primary_site) |>    dplyr::summarise(num_terms = dplyr::n(),                    .groups = \"drop\") |>   dplyr::arrange(dplyr::desc(num_terms))) #>                 primary_site num_terms #> 1                   Lymphoid      4037 #> 2                Soft Tissue      2828 #> 3                  CNS/Brain      2294 #> 4              Head and Neck      2273 #> 5                       Skin      1817 #> 6                    Myeloid      1777 #> 7                       Lung      1086 #> 8               Colon/Rectum       966 #> 9       Ovary/Fallopian Tube       851 #> 10                    Breast       781 #> 11         Esophagus/Stomach       719 #> 12                      Bone       551 #> 13     Bladder/Urinary Tract       482 #> 14                    Uterus       451 #> 15             Biliary Tract       416 #> 16                     Liver       415 #> 17                    Kidney       396 #> 18                  Pancreas       343 #> 19 Peripheral Nervous System       292 #> 20                    Cervix       287 #> 21                       Eye       274 #> 22              Vulva/Vagina       265 #> 23                   Thyroid       250 #> 24                    Testis       239 #> 25                  Prostate       207 #> 26             Other/Unknown       176 #> 27                    Pleura       124 #> 28                Peritoneum        99 #> 29                    Thymus        87 #> 30             Adrenal Gland        70 #> 31                     Penis        61 #> 32          Ampulla of Vater        46"},{"path":"https://sigven.github.io/phenOncoX/articles/phenOncoX.html","id":"get-all-oncotree-expanded-cancer-phenotype-terms-relevant-for-prostate-cancer","dir":"Articles","previous_headings":"Get OncoTree terms","what":"Get all (OncoTree-expanded) cancer phenotype terms relevant for prostate cancer","title":"Getting started","text":"","code":"## get all oncoterms for prostate cancer oncoterms_prostate <- phenOncoX::get_terms(   cache_dir = download_dir,    site = \"Prostate\")  ## Make as datatable prostate_terms_table <- DT::datatable(   dplyr::select(     oncoterms_prostate$records,      primary_site, cui, cui_name,     dplyr::everything()),   escape = FALSE,   extensions = c(\"Buttons\", \"Responsive\"),    width = \"100%\",   options = list(     buttons = c(\"csv\", \"excel\"),      dom = \"Bfrtip\"))"},{"path":"https://sigven.github.io/phenOncoX/articles/phenOncoX.html","id":"session-info","dir":"Articles","previous_headings":"","what":"Session Info","title":"Getting started","text":"","code":"# set eval = FALSE if you don't want this info (useful for reproducibility)  # to appear sessionInfo() #> R version 4.4.1 (2024-06-14) #> Platform: x86_64-pc-linux-gnu #> Running under: Ubuntu 22.04.5 LTS #>  #> Matrix products: default #> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  #> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 #>  #> locale: #>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        #>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8    #>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C           #> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C    #>  #> time zone: UTC #> tzcode source: system (glibc) #>  #> attached base packages: #> [1] stats     graphics  grDevices utils     datasets  methods   base      #>  #> loaded via a namespace (and not attached): #>  [1] jsonlite_1.8.9    dplyr_1.1.4       compiler_4.4.1    crayon_1.5.3      #>  [5] tidyselect_1.2.1  phenOncoX_0.8.0   jquerylib_0.1.4   systemfonts_1.1.0 #>  [9] textshaping_0.4.0 yaml_2.3.10       fastmap_1.2.0     R6_2.5.1          #> [13] generics_0.1.3    curl_5.2.3        knitr_1.48        htmlwidgets_1.6.4 #> [17] tibble_3.2.1      desc_1.4.3        bslib_0.8.0       pillar_1.9.0      #> [21] rlang_1.1.4       DT_0.33           utf8_1.2.4        cachem_1.1.0      #> [25] lgr_0.4.4         xfun_0.48         fs_1.6.4          sass_0.4.9        #> [29] cli_3.6.3         withr_3.0.1       pkgdown_2.1.1     magrittr_2.0.3    #> [33] crosstalk_1.2.1   digest_0.6.37     lifecycle_1.0.4   vctrs_0.6.5       #> [37] evaluate_1.0.1    gargle_1.5.2      glue_1.8.0        ragg_1.3.3        #> [41] googledrive_2.1.1 fansi_1.0.6       httr_1.4.7        rmarkdown_2.28    #> [45] purrr_1.0.2       tools_4.4.1       pkgconfig_2.0.3   htmltools_0.5.8.1"},{"path":[]},{"path":"https://sigven.github.io/phenOncoX/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Sigve Nakken. Author, maintainer.","code":""},{"path":"https://sigven.github.io/phenOncoX/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Nakken S (2024). phenOncoX: phenotype ontology map cancer. R package version 0.8.0, https://sigven.github.io/phenOncoX.","code":"@Manual{,   title = {phenOncoX: A phenotype ontology map for cancer},   author = {Sigve Nakken},   year = {2024},   note = {R package version 0.8.0},   url = {https://sigven.github.io/phenOncoX}, }"},{"path":"https://sigven.github.io/phenOncoX/index.html","id":"phenoncox-","dir":"","previous_headings":"","what":"A phenotype ontology map for cancer","title":"A phenotype ontology map for cancer","text":"ontological definition disease enables type disease singularly classified formalized structure. intention, use disease ontology terms facilitate cross-link information separate disease-related knowledge resources given domain. However, multiple disease ontology frameworks developed human disease (.e. OncoTree, Experimental Factor Ontology (EFO), Disease Ontology (), UMLS, ICD-10), used different extents across knowledge resources oncology domain, following: gene-disease associations drug-disease indications variant-disease associations order integrate knowledge resources, henceforth need cross-link map entries across disease ontologies extent possible. phenOncoX R data package attempts address challenge. short, phenOncoX provides global cross-mapped set phenotype ontology terms attributed cancer phenotypes. mapping established within phenOncoX semi-manually curated, using OncoTree starting point list UMLS phenotype terms per cancer subtype/primary site. Next, phenOncoX appends number phenotypes attributed heritable cancer conditions. Furthermore, cancer subtype entry OncoTree expanded additional subtypes found UMLS child-parent hierarchy disease terms. entry final list phenotype terms, make cross-mappings phenotype terms EFO, , ICD10 classification. late October 2024, following ontology versions used create mapping: OncoTree (2021_11_02) Experimental Factor Ontology v3.71.0 (2024-10-15) Disease Ontology (v2024-09-27) package offers pre-processed datasets, along metadata, user can retrieve use projects set-ups. package utilizes googledrive R package download pre-processed documented datasets local cache directory provided user. IMPORTANT NOTE: mapping established phenOncoX attempts comprehensive, acknowledge presence missing erroneous cross-references might still occur.","code":""},{"path":"https://sigven.github.io/phenOncoX/index.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting started","title":"A phenotype ontology map for cancer","text":"Installation instructions Usage examples","code":""},{"path":"https://sigven.github.io/phenOncoX/index.html","id":"contact","dir":"","previous_headings":"","what":"Contact","title":"A phenotype ontology map for cancer","text":"sigven ifi.uio.","code":""},{"path":"https://sigven.github.io/phenOncoX/index.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"A phenotype ontology map for cancer","text":"Please note project released Contributor Code Conduct. participating project agree abide terms.","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_aux_maps.html","id":null,"dir":"Reference","previous_headings":"","what":"Get auxiliary phenotype ontology maps — get_aux_maps","title":"Get auxiliary phenotype ontology maps — get_aux_maps","text":"Downloads returns multiple phenotype dictionaries used cross-referencing terms, including UMLS, EFO, , ICD10. dataset comes list object, two elements: metadata - data frame metadata regarding annotation resources used records - list object multiple lists/data.frames","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_aux_maps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get auxiliary phenotype ontology maps — get_aux_maps","text":"","code":"get_aux_maps(cache_dir = NA, force_download = FALSE)"},{"path":"https://sigven.github.io/phenOncoX/reference/get_aux_maps.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get auxiliary phenotype ontology maps — get_aux_maps","text":"cache_dir Local directory data download force_download Logical indicating local cache overwritten (set TRUE re-download file exists cache)","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_aux_maps.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get auxiliary phenotype ontology maps — get_aux_maps","text":"metadata - data frame 4 rows 6 columns: source - gene annotation source annotation_data - type annotations used url - URL annotation resource citation - publication cite annotation source (citation; PMID) version - version used abbreviation - abbreviation used column names records records - list following elements: umls - List UMLS data dictionaries - Data frame identifiers/names efo - List EFO data dictionaries icd10 - Data frame CUI ICD10 cross-reference","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_aux_maps.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get auxiliary phenotype ontology maps — get_aux_maps","text":"","code":"if (FALSE) { # \\dontrun{ library(phenOncoX) oncology_terms <- get_aux_maps(cache_dir = tempdir()) } # }"},{"path":"https://sigven.github.io/phenOncoX/reference/get_pox_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Function that retrieves phenOncoX data from Google Drive/local cache — get_pox_data","title":"Function that retrieves phenOncoX data from Google Drive/local cache — get_pox_data","text":"Function retrieves phenOncoX data Google Drive/local cache","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_pox_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function that retrieves phenOncoX data from Google Drive/local cache — get_pox_data","text":"","code":"get_pox_data(cache_dir = NA, force_download = FALSE, db = \"oncotree_core\")"},{"path":"https://sigven.github.io/phenOncoX/reference/get_pox_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function that retrieves phenOncoX data from Google Drive/local cache — get_pox_data","text":"cache_dir Local directory data download force_download Logical indicating local cache overwritten (set TRUE re-download file exists cache) db type dataset retrieved","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_pox_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function that retrieves phenOncoX data from Google Drive/local cache — get_pox_data","text":"pre-processed ontology terms records/metadata auxiliary maps","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_terms.html","id":null,"dir":"Reference","previous_headings":"","what":"Get oncology-relevant phenotype terms — get_terms","title":"Get oncology-relevant phenotype terms — get_terms","text":"Downloads returns dataset expanded set oncology-relevant phenotype terms (UMLS), using OncoTree starting point. expansion conducted tracking MeSH/UMLS tree structure phenotype terms. record comes cross-references Disease Ontology (), Experimental Factor Ontology (EFO), ICD10 wherever available. dataset comes list object, two elements: metadata - data frame metadata regarding annotation resources used records - data frame phenotype terms","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_terms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get oncology-relevant phenotype terms — get_terms","text":"","code":"get_terms(   cache_dir = NA,   force_download = FALSE,   site = NA,   ignore_minor_type = FALSE )"},{"path":"https://sigven.github.io/phenOncoX/reference/get_terms.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get oncology-relevant phenotype terms — get_terms","text":"cache_dir Local directory data download force_download Logical indicating local cache overwritten (set TRUE re-download file exists cache) site limit phenotype terms relevant given primary tumor type/site. Possible values: 'Adrenal Gland', 'Ampulla Vater', 'Biliary Tract', 'Bladder/Urinary Tract', 'Bone', 'Breast', 'Cervix', 'CNS/Brain', 'Colon/Rectum', 'Esophagus/Stomach', 'Eye', 'Head Neck', 'Kidney', 'Liver', 'Lung', 'Lymphoid', 'Myeloid', '/Unknown', 'Ovary/Fallopian Tube', 'Pancreas', 'Penis', 'Peripheral Nervous System', 'Peritoneum', 'Pleura', 'Prostate', 'Skin', 'Soft Tissue', 'Testis', 'Thymus', 'Thyroid', 'Uterus', 'Vulva/Vagina' ignore_minor_type logical indicating minor tumor types excluded ","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_terms.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get oncology-relevant phenotype terms — get_terms","text":"metadata - data frame 5 rows 6 columns: source - gene annotation source annotation_data - type annotations used url - URL annotation resource citation - publication cite annotation source (citation; PMID) version - version used abbreviation - abbreviation used column names records records - data frame following columns: primary_site - Primary tumor type/site ot_main_type - Main tumor type (OncoTree) ot_name - Phenotype name (OncoTree) ot_level - Tree level (OncoTree) ot_code - Phenotype code (OncoTree) ot_code_path - Tree code path (OncoTree) cui - Concept unique identifier (UMLS) cui_name - Phenotype name (UMLS) efo_id - EFO identifier efo_name - EFO name do_id - identifier do_name - name do_cancer_slim - identifier part cancer slim dictionary (TRUE/FALSE) minor_type - logical indicating whether term part minor tumor type/site icd10_code - ICD10 identifier source - term indicating dataset source","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_terms.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get oncology-relevant phenotype terms — get_terms","text":"","code":"if (FALSE) { # \\dontrun{ library(phenOncoX) oncology_terms <- get_terms(cache_dir = tempdir()) } # }"},{"path":"https://sigven.github.io/phenOncoX/reference/get_tree.html","id":null,"dir":"Reference","previous_headings":"","what":"Get core phenotype terms from OncoTree — get_tree","title":"Get core phenotype terms from OncoTree — get_tree","text":"Downloads returns dataset curated phenotype terms (UMLS) OncoTree. dataset comes list object, two elements: metadata - data frame metadata regarding annotation resources used records - data frame phenotype terms","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_tree.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get core phenotype terms from OncoTree — get_tree","text":"","code":"get_tree(   cache_dir = NA,   force_download = FALSE,   site = NA,   max_tree_depth = 6,   ignore_minor_type = FALSE )"},{"path":"https://sigven.github.io/phenOncoX/reference/get_tree.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get core phenotype terms from OncoTree — get_tree","text":"cache_dir Local directory data download force_download Logical indicating local cache overwritten (set TRUE re-download file exists cache) site limit OncoTree terms relevant given primary tumor type/site. Possible values: 'Adrenal Gland', 'Ampulla Vater', 'Biliary Tract', 'Bladder/Urinary Tract', 'Bone', 'Breast', 'Cervix', 'CNS/Brain', 'Colon/Rectum', 'Esophagus/Stomach', 'Eye', 'Head Neck', 'Kidney', 'Liver', 'Lung', 'Lymphoid', 'Myeloid', '/Unknown', 'Ovary/Fallopian Tube', 'Pancreas', 'Penis', 'Peripheral Nervous System', 'Peritoneum', 'Pleura', 'Prostate', 'Skin', 'Soft Tissue', 'Testis', 'Thymus', 'Thyroid', 'Uterus', 'Vulva/Vagina' max_tree_depth consider terms given depth OncoTree (integer 1-6, default: 6) ignore_minor_type logical indicating minor tumor types excluded ","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_tree.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get core phenotype terms from OncoTree — get_tree","text":"metadata - data frame 1 row 6 columns: source - gene annotation source annotation_data - type annotations used url - URL annotation resource citation - publication cite annotation source (citation; PMID) version - version used abbreviation - abbreviation used column names records records - data frame following columns: primary_site - Primary tumor type/site ot_main_type - Main tumor type (OncoTree) ot_name - Phenotype name (OncoTree) ot_level - Tree level (OncoTree) ot_code - Phenotype code (OncoTree) ot_code_path - Tree code path (OncoTree) cui - Concept unique identifier (UMLS) cui_name - Phenotype name (UMLS) minor_type - logical indicating whether term part minor tumor type/site source - term indicating dataset source","code":""},{"path":"https://sigven.github.io/phenOncoX/reference/get_tree.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get core phenotype terms from OncoTree — get_tree","text":"","code":"if (FALSE) { # \\dontrun{ library(phenOncoX) oncology_terms <- get_tree(cache_dir = tempdir()) } # }"},{"path":"https://sigven.github.io/phenOncoX/reference/tidyeval.html","id":null,"dir":"Reference","previous_headings":"","what":"Tidy eval helpers — tidyeval","title":"Tidy eval helpers — tidyeval","text":"https://cran.r-project.org/web/packages/dplyr/vignettes/programming.html","code":""}]