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<div class="title">IDDecoyProbability </div> </div>
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<div class="textblock"><p>Util to estimate probability of peptide hits</p>
<center> <table class="doxtable">
<tr>
<td align="center" bgcolor="#EBEBEB">pot. predecessor tools </td><td valign="middle" rowspan="3"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> IDDecoyProbability <img class="formulaInl" alt="$ \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">- </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_PeptideIndexer.html">PeptideIndexer</a> </td></tr>
</table>
</center><dl class="experimental"><dt><b><a class="el" href="experimental.html#_experimental000026">Experimental classes:</a></b></dt><dd>This util is deprecated and might behave not as expected!</dd></dl>
<p>So far an estimation of the false score distribution with a gamma distribution and the correct score distribution with a gaussian distribution is performed. The probabilities are calculated using bayes law, similar to PeptideProphet. This implementation is much simpler than that of PeptideProphet.</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
IDDecoyProbability -- Estimates peptide probabilities using a decoy search strategy.
WARNING: This util is deprecated.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
IDDecoyProbability <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 of combined forward decoy search (reindex with PeptideIndexer first
) (valid formats: 'idXML')
-fwd_in <file> Identification input of forward run (valid formats: 'idXML')
-rev_in <file> Identification input of decoy run (valid formats: 'idXML')
-out <file>* Identification output with forward scores converted to probabilities (valid formats:
'idXML')
Common UTIL 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:
- decoy_algorithm Algorithm parameter subsection
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">+IDDecoyProbability</span><span class="node_description">Estimates peptide probabilities using a decoy search strategy.<br>WARNING: This util is deprecated.</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 'IDDecoyProbability'</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 of combined forward decoy search (reindex with PeptideIndexer first)</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 of 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 of 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 forward scores converted to probabilities</span><span class="item_tags">output file</span><span class="item_restrictions">*.idXML</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">+++decoy_algorithm</span><span class="node_description">Algorithm parameter subsection</span></div>
<div class="item item_advanced"><span class="item_name" style="padding-left:32px;">number_of_bins</span><span class="item_value">40</span>
<span class="item_description">Number of bins used for the fitting, if sparse datasets are used, this number should be smaller</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">lower_score_better_default_value_if_zero</span><span class="item_value">50</span>
<span class="item_description">This value is used if e.g. a E-value score is 0 and cannot be transformed in a real number (log of E-value)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div></div>
<p>For the parameters of the algorithm section see the algorithms documentation: <br/>
<a class="el" href="classOpenMS_1_1IDDecoyProbability.html">decoy_algorithm</a> <br/>
</p>
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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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