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<div class="title">ConsensusID </div> </div>
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<div class="textblock"><p>Computes a consensus identification from peptide identification engines.</p>
<center> <table class="doxtable">
<tr>
<td align="center" bgcolor="#EBEBEB">potential predecessor tools </td><td valign="middle" rowspan="4"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> ConsensusID <img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> </td><td align="center" bgcolor="#EBEBEB">potential 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="3"><a class="el" href="TOPP_FalseDiscoveryRate.html">FalseDiscoveryRate</a> </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_IDPosteriorErrorProbability.html">IDPosteriorErrorProbability</a> </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_IDMapper.html">IDMapper</a> </td></tr>
</table>
</center><p>This implementation (for PEPMatrix and PEPIons) is described in </p>
<p>Nahnsen S, Bertsch A, Rahnenfuehrer J, Nordheim A, Kohlbacher O<br/>
Probabilistic Consensus Scoring Improves Tandem Mass Spectrometry Peptide Identification<br/>
Journal of Proteome Research (2011), DOI: 10.1021/pr2002879<br/>
</p>
<p>The input file can contain several searches, e.g., from several identification engines. In order to use the PEPMatrix or the PEPIons algorithm, posterior error probabilities (PEPs) need to be calculated using the <a class="el" href="TOPP_IDPosteriorErrorProbability.html">IDPosteriorErrorProbability</a> tool for all individual search engines. After PEP calculation, the different search engine results have to be combined using <a class="el" href="TOPP_IDMerger.html">IDMerger</a>. Identification runs can be mapped to featureXML and consensusXML with the <a class="el" href="TOPP_IDMapper.html">IDMapper</a> tool. The merged file can now be fed into into the <a class="el" href="TOPP_ConsensusID.html">ConsensusID</a> tool. For the statistical assessment of the results it is recommended to use target-decoy databases for peptide identifications. The false discovery rates (FDRs) can be calculated using the <a class="el" href="TOPP_FalseDiscoveryRate.html">FalseDiscoveryRate</a> tool.</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
ConsensusID -- Computes a consensus identification from peptide identifications of several identification
engines.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
ConsensusID <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>* Input file (valid formats: 'idXML', 'featureXML', 'consensusXML')
-out <file>* Output file (valid formats: 'idXML', 'featureXML', 'consensusXML')
-rt_delta <value> Maximum allowed precursor RT deviation between identifications. (default: '0.1' min:
'0')
-mz_delta <value> Maximum allowed precursor m/z deviation between identifications. (default: '0.1' min:
'0')
-min_length <value> Minimum of length of peptides for final consensus list (default: '6' min: '1')
-use_all_hits If 'true' not only the first hit, but all are used (peptides only)
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 Consensus algorithm section
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">+ConsensusID</span><span class="node_description">Computes a consensus identification from peptide identifications of several identification engines.</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 'ConsensusID'</span></div>
<div class="item"><span class="item_name item_required" style="padding-left:24px;">in</span><span class="item_value"></span>
<span class="item_description">input file</span><span class="item_tags">input file</span><span class="item_restrictions">*.idXML,*.featureXML,*.consensusXML</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">output file</span><span class="item_tags">output file</span><span class="item_restrictions">*.idXML,*.featureXML,*.consensusXML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">rt_delta</span><span class="item_value">0.1</span>
<span class="item_description">Maximum allowed precursor RT deviation between identifications.</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">mz_delta</span><span class="item_value">0.1</span>
<span class="item_description">Maximum allowed precursor m/z deviation between identifications.</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">min_length</span><span class="item_value">6</span>
<span class="item_description">Minimum of length of peptides for final consensus list</span><span class="item_tags"></span><span class="item_restrictions">1:∞</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">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 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">Consensus algorithm section</span></div>
<div class="item"><span class="item_name" style="padding-left:32px;">algorithm</span><span class="item_value">PEPMatrix</span>
<span class="item_description">Algorithm used for the consensus scoring.<br>ranked -- reorders the hits according to a consensus score computed from the ranks in the input runs. The score is normalized to the interval (0,100). The PeptideIdentifications do not need to have the same score type.<br>average -- reorders the hits according to the average score of the input runs. Make sure to use PeptideIdentifications with the same score type only!<br>PEPMatrix -- calculates a consensus score based on posterior error probabilities and scoring matrices for siimilarity. This algorithm uses the PAM30MS matrix to score sequences not listed by all engines. Make sure to use PeptideIdentifications with score types converted to PEPs only!<br>PEPIons -- calculates a consensus score based on posterior error probabilities and fragment ion siimilarity. Make sure to use PeptideIdentifications with score types converted to PEPs only!<br>Minimum -- calculates a consensus score based on the minimal score. Make sure to use PeptideIdentifications with score types converted to PEPs only!<br></span><span class="item_tags"></span><span class="item_restrictions">ranked,average,PEPMatrix,PEPIons,Minimum</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">considered_hits</span><span class="item_value">10</span>
<span class="item_description">The number of top hits that are used for the consensus scoring.</span><span class="item_tags"></span><span class="item_restrictions">1:∞</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">number_of_runs</span><span class="item_value">0</span>
<span class="item_description">The number of runs used as input. This information is used in 'Ranked' and 'Average' to compute the new scores. If not given, the number of input identifications is taken.</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="node"><span class="node_name">++++PEPIons</span><span class="node_description"></span></div>
<div class="item"><span class="item_name" style="padding-left:40px;">MinNumberOfFragments</span><span class="item_value">2</span>
<span class="item_description">The minimal number of similar (between two suggested sequences) fragment ion masses that is necessary to evaluate the shared peak count similarity (SPC).</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">common</span><span class="item_value">1.1</span>
<span class="item_description">Similarity threshold to accept the best score. E.g. for a given spectrum: engine 1 -> pep 1 with score x1 and engine2 -> pep2 with score x2. The better score from {x1,x2} will be used if the degree of similarity between pep1 and pep2 >= common, Note that 0 <= degree of similarity <= 1. Values > 1 will disable this option.</span><span class="item_tags"></span><span class="item_restrictions">0:1.1</span></div> <div class="node"><span class="node_name">++++PEPMatrix</span><span class="node_description"></span></div>
<div class="item"><span class="item_name" style="padding-left:40px;">common</span><span class="item_value">1.1</span>
<span class="item_description">Similarity threshold to accept the best score. E.g. for a given spectrum: engine 1 -> pep 1 with score x1 and engine2 -> pep2 with score x2. The better score from {x1,x2} will be used if the degree of similarity between pep1 and pep2 >= common, Note that 0 <= degree of similarity <= 1. Values > 1 will disable this option.</span><span class="item_tags"></span><span class="item_restrictions">0:1.1</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">penalty</span><span class="item_value">5</span>
<span class="item_description">Give the gap penalty (the same penalty will be used for opening and extension) as a positive integer</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_1ConsensusID.html">Consensus 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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