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<div class="title">FalseDiscoveryRate </div> </div>
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<div class="textblock"><p>Tool to estimate the false discovery rate on peptide and protein level </p>
<center></center><center><table class="doxtable">
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<td align="center" bgcolor="#EBEBEB">pot. predecessor tools </td><td valign="middle" rowspan="3"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> FalseDiscoveryRate <img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> </td><td align="center" bgcolor="#EBEBEB">pot. successor tools </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_MascotAdapter.html">MascotAdapter</a> (or other ID engines) </td><td valign="middle" align="center" rowspan="2"><a class="el" href="TOPP_IDFilter.html">IDFilter</a> </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_PeptideIndexer.html">PeptideIndexer</a> </td></tr>
</table>
</center><p>This TOPP tool can calculate the false discovery rate (FDR) given a forward and backward search (or one run on a combined database). Most useful is this on protein level, however, it also can be applied to peptides.</p>
<p>The false discovery rate is defined as the number of false discoveries (the hits in the reversed search) over the number of false and correct discoveries (the hits in both databases) with a score better than a given threshold.</p>
<p>Prerequisites:</p>
<ul>
<li>When using a combined database of forward and reverse hits (thus only using one search run per ID engine), then use <a class="el" href="TOPP_PeptideIndexer.html">PeptideIndexer</a> to index an idXML file generated by a search engine adapter, e.g. <a class="el" href="TOPP_MascotAdapter.html">MascotAdapter</a>. This will allow us to discern which peptides are from the target vs. decoy database.</li>
</ul>
<p>When no decoy hits were found you will get a warning saying something like:<br/>
"FalseDiscoveryRate: #decoy sequences is zero! Setting all target sequences to q-value/FDR 0!"<br/>
This should be a serious concern, since the target/decoy annotation in a previous step has probably a misconfigured database (see <a class="el" href="TOPP_PeptideIndexer.html">PeptideIndexer</a>).</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
FalseDiscoveryRate -- Estimates the false discovery rate on peptide and protein level using decoy searches.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
FalseDiscoveryRate <options>
This tool has algoritm parameters that are not shown here! Please check the ini file for a detailed descripti
on or use the --helphelp option.
Options (mandatory options marked with '*'):
-in <file> Identification input file which contains a search against a concatenated sequence databa
se. Either specify '-in' alone or 'fwd_in' together with 'rev_in' as input. (valid forma
ts: 'idXML')
-fwd_in <file> Identification input to estimate FDR, forward run. (valid formats: 'idXML')
-rev_in <file> Identification input to estimate FDR, decoy run. (valid formats: 'idXML')
-out <file>* Identification output with annotated FDR (valid formats: 'idXML')
-proteins_only If set, the FDR of the proteins only is calculated
-peptides_only If set, the FDR of the peptides only is calculated
Common TOPP options:
-ini <file> Use the given TOPP INI file
-threads <n> Sets the number of threads allowed to be used by the TOPP tool (default: '1')
-write_ini <file> Writes the default configuration file
--help Shows options
--helphelp Shows all options (including advanced)
The following configuration subsections are valid:
- algorithm Parameter section for the FDR calculation algorithm
You can write an example INI file using the '-write_ini' option.
Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor.
Have a look at the OpenMS documentation for more information.
</pre><p> <b>INI file documentation of this tool:</b> <div class="ini_global">
<div class="legend">
<b>Legend:</b><br>
<div class="item item_required">required parameter</div>
<div class="item item_advanced">advanced parameter</div>
</div>
<div class="node"><span class="node_name">+FalseDiscoveryRate</span><span class="node_description">Estimates the false discovery rate on peptide and protein level using decoy searches.</span></div>
<div class="item item_advanced"><span class="item_name" style="padding-left:16px;">version</span><span class="item_value">1.11.1</span>
<span class="item_description">Version of the tool that generated this parameters file.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="node"><span class="node_name">++1</span><span class="node_description">Instance '1' section for 'FalseDiscoveryRate'</span></div>
<div class="item"><span class="item_name" style="padding-left:24px;">in</span><span class="item_value"></span>
<span class="item_description">Identification input file which contains a search against a concatenated sequence database. Either specify '-in' alone or 'fwd_in' together with 'rev_in' as input.</span><span class="item_tags">input file</span><span class="item_restrictions">*.idXML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">fwd_in</span><span class="item_value"></span>
<span class="item_description">Identification input to estimate FDR, forward run.</span><span class="item_tags">input file</span><span class="item_restrictions">*.idXML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">rev_in</span><span class="item_value"></span>
<span class="item_description">Identification input to estimate FDR, decoy run.</span><span class="item_tags">input file</span><span class="item_restrictions">*.idXML</span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">out</span><span class="item_value"></span>
<span class="item_description">Identification output with annotated FDR</span><span class="item_tags">output file</span><span class="item_restrictions">*.idXML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">proteins_only</span><span class="item_value">false</span>
<span class="item_description">If set, the FDR of the proteins only is calculated</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">peptides_only</span><span class="item_value">false</span>
<span class="item_description">If set, the FDR of the peptides only is calculated</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">log</span><span class="item_value"></span>
<span class="item_description">Name of log file (created only when specified)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">debug</span><span class="item_value">0</span>
<span class="item_description">Sets the debug level</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">threads</span><span class="item_value">1</span>
<span class="item_description">Sets the number of threads allowed to be used by the TOPP tool</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">no_progress</span><span class="item_value">false</span>
<span class="item_description">Disables progress logging to command line</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">test</span><span class="item_value">false</span>
<span class="item_description">Enables the test mode (needed for internal use only)</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="node"><span class="node_name">+++algorithm</span><span class="node_description">Parameter section for the FDR calculation algorithm</span></div>
<div class="item"><span class="item_name" style="padding-left:32px;">q_value</span><span class="item_value">true</span>
<span class="item_description">If 'true', the q-values will be calculated instead of the FDRs</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">use_all_hits</span><span class="item_value">false</span>
<span class="item_description">If 'true' not only the first hit, but all are used (peptides only)</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">split_charge_variants</span><span class="item_value">false</span>
<span class="item_description">If set to 'true' charge variants are treated separately (for peptides of combined target/decoy searches only).</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">treat_runs_separately</span><span class="item_value">false</span>
<span class="item_description">If set to 'true' different search runs are treated separately (for peptides of combined target/decoy searches only).</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">decoy_string</span><span class="item_value">_rev</span>
<span class="item_description">String which is appended at the accession of the protein to indicate that it is a decoy protein (for proteins only).</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">add_decoy_peptides</span><span class="item_value">false</span>
<span class="item_description">If set to true, decoy peptides will be written to output file, too. The q-value is set to the closest target score.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div></div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5</font></TD>
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