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assign-confidence.html
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<!-- START CONTENT -->
<h1>assign-confidence</h1>
<h2>Usage:</h2>
<p><code>crux assign-confidence [options] <target input>+</code></p>
<h2>Description:</h2>
<p>Given target and decoy scores, estimate a q-value for each target score. The q-value is analogous to a p-value but incorporates false discovery rate multiple testing correction. The q-value associated with a score threshold T is defined as the minimal false discovery rate (FDR) at which a score of T is deemed significant. In this setting, the q-value accounts for the fact that we are analyzing a large collection of scores. For confidence estimation afficionados, please note that this definition of "q-value" is independent of the notion of "positive FDR" as defined in (Storey <em>Annals of Statistics</em> 31:2013-2015:2003).</p><p>To estimate FDRs, <code>assign-confidence</code> uses one of two different procedures. Both require that the input contain both target and decoy scores. The default, target-decoy competition (TDC) procedure is described in this article:</p><blockquote>Josh E. Elias and Steve P. Gygi. "Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry." <em>Nature Methods</em>. 4(3):207-14, 2007.</blockquote><p>Note that <code>assign-confidence</code> implements a variant of the protocol proposed by Elias and Gygi: rather than reporting a list that contains both targets and decoys, <code>assign-confidence</code> reports only the targets. The FDR estimate is adjusted accordingly (by dividing by 2).</p><p>The alternative, <em>mix-max</em> procedure is described in this article:</p><blockquote>Uri Keich, Attila Kertesz-Farkas and William Stafford Noble. <a href="http://pubs.acs.org/doi/abs/10.1021/acs.jproteome.5b00081">"An improved false discovery rate estimation procedure for shotgun proteomics."</a> <i>Journal of Proteome Research</i>. 14(8):3148-3161, 2015.</blockquote><p>Note that the mix-max procedure requires as input calibrated scores, such as Comet E-values or p-values produced using Tide-s <code>exact-p-value</code> option.</p><p>The mix-max procedure requires that scores are reported from separate target and decoy searches. Thus, this approach is incompatible with a search that is run using the <code>--concat T</code> option to <code>tide-search</code> or the <code>--decoy_search 2</code> option to <code>comet</code>. On the other hand, the TDC procedure can take as input searches conducted in either mode (concatenated or separate). If given separate search results and asked to do TDC estimation, <code>assign-confidence</code> will carry out the target-decoy competition as part of the confidence estimation procedure.</p><p>In each case, the estimated FDRs are converted to q-values by sorting the scores then taking, for each score, the minimum of the current FDR and all of the FDRs below it in the ranked list.</p><p>A primer on multiple testing correction can be found here:</p><blockquote>William Stafford Noble. <a href="http://www.nature.com/nbt/journal/v27/n12/full/nbt1209-1135.html">"How does multiple testing correction work?"</a> <em>Nature Biotechnology</em>. 27(12):1135-1137, 2009.</blockquote>
<h2>Input:</h2>
<ul>
<li><code>target input+</code> – One or more files, each containing a collection of peptide-spectrum matches (PSMs) in <a href="../file-formats/txt-format.html">tab-delimited text</a>, <a href="http://tools.proteomecenter.org/wiki/index.php?title=Formats:pepXML">PepXML</a>, or <a href="http://www.psidev.info/mzidentml">mzIdentML</a> format. In tab-delimited text format, only the specified score column is required. However if --estimation-method is tdc, then the columns "scan" and "charge" are required, as well as "protein ID" if the search was run with concat=F. Furthermore, if the --estimation-method is specified to peptide-level is set to T, then the column "peptide" must be included, and if --sidak is set to T, then the "distinct matches/spectrum" column must be included.<br>Note that multiple files can also be provided either on the command line or using the --list-of-files option.<br>Decoys can be provided in two ways: either as a separate file or embedded within the same file as the targets. Crux will first search the given file for decoys using a prefix (specified via --decoy-prefix) on the protein name. If no decoys are found, then Crux will search for decoys in a separate file. The decoy file name is constructed from the target file name by replacing "target" with "decoy". For example, if tide-search.target.txt is provided as input, then Crux will search for a corresponding file named "tide-search.decoy.txt."<br>Note that if decoys are provided in a separate file, then assign-confidence will first carry out a target-decoy competition, identifying corresponding pairs of targets and decoys and eliminating the one with the worse score. In this case, the column/tag called "delta_cn" will be eliminated from the output.</li>
</ul>
<h2>Output:</h2>
<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
<ul>
<li><code>assign-confidence.target.txt</code> – a <a href="../file-formats/txt-format.html">tab-delimited text file</a> that contains the targets, sorted by score. The file will contain one new column, named "<method> q-value", where <method> is either "tdc" or "mix-max".</li>
<li><code>assign-confidence.log.txt</code> – a log file containing a copy of all messages that were printed to stderr.</li>
<li><code>assign-confidence.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
</ul>
<h2>Options:</h2>
<ul style="list-style-type: none;">
<li class="nobullet">
<h3>assign-confidence options</h3>
<ul>
<li class="nobullet"><code>--estimation-method mix-max|tdc|peptide-level</code> – Specify the method used to estimate q-values. The mix-max procedure or target-decoy competition apply to PSMs. The peptide-level option eliminates any PSM for which there exists a better scoring PSM involving the same peptide, and then uses decoys to assign confidence estimates. Default = <code>tdc</code>.</li>
<li class="nobullet"><code>--score <string></code> – Specify the column (for tab-delimited input) or tag (for XML input) used as input to the q-value estimation procedure. If this parameter is unspecified, then the program searches for "xcorr score", "evalue" (comet), "exact p-value" score fields in this order in the input file. Default = <code><empty></code>.</li>
<li class="nobullet"><code>--sidak T|F</code> – Adjust the score using the Sidak adjustment and reports them in a new column in the output file. Note that this adjustment only makes sense if the given scores are p-values, and that it requires the presence of the "distinct matches/spectrum" feature for each PSM. Default = <code>false</code>.</li>
<li class="nobullet"><code>--combine-charge-states T|F</code> – Specify this parameter to T in order to combine charge states with peptide sequencesin peptide-centric search. Works only if estimation-method = peptide-level. Default = <code>false</code>.</li>
<li class="nobullet"><code>--combine-modified-peptides T|F</code> – Specify this parameter to T in order to treat peptides carrying different or no modifications as being the same. Works only if estimation = peptide-level. Default = <code>false</code>.</li>
</ul>
</li>
<li class="nobullet">
<h3>Input and output</h3>
<ul>
<li class="nobullet"><code>--decoy-prefix <string></code> – Specifies the prefix of the protein names that indicate a decoy. Default = <code>decoy_</code>.</li>
<li class="nobullet"><code>--verbosity <integer></code> – Specify the verbosity of the current processes. Each level prints the following messages, including all those at lower verbosity levels: 0-fatal errors, 10-non-fatal errors, 20-warnings, 30-information on the progress of execution, 40-more progress information, 50-debug info, 60-detailed debug info. Default = <code>30</code>.</li>
<li class="nobullet"><code>--parameter-file <string></code> – A file containing parameters. See the <a href="../file-formats/parameter-file.html">parameter documentation</a> page for details. Default = <code><empty></code>.</li>
<li class="nobullet"><code>--overwrite T|F</code> – Replace existing files if true or fail when trying to overwrite a file if false. Default = <code>false</code>.</li>
<li class="nobullet"><code>--output-dir <string></code> – The name of the directory where output files will be created. Default = <code>crux-output</code>.</li>
<li class="nobullet"><code>--list-of-files T|F</code> – Specify that the search results are provided as lists of files, rather than as individual files. Default = <code>false</code>.</li>
<li class="nobullet"><code>--fileroot <string></code> – The fileroot string will be added as a prefix to all output file names. Default = <code><empty></code>.</li>
</ul>
</li>
</ul>
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The original version of Crux was written by Chris Park and Aaron Klammer
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