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<div class="title">RTPredict </div> </div>
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<div class="textblock"><p>This application is used to predict retention times for peptides or peptide separation.</p>
<p>This methods and applications of this model are described in several publications:</p>
<p>Nico Pfeifer, Andreas Leinenbach, Christian G. Huber and Oliver Kohlbacher Statistical learning of peptide retention behavior in chromatographic separations: A new kernel-based approach for computational proteomics. BMC Bioinformatics 2007, 8:468</p>
<p>Nico Pfeifer, Andreas Leinenbach, Christian G. Huber and Oliver Kohlbacher Improving Peptide Identification in Proteome Analysis by a Two-Dimensional Retention Time Filtering Approach J. Proteome Res. 2009, 8(8):4109-15</p>
<p>The input of this application is an svm model and an idXML file with peptide identifications. The svm model file is specified by the <b>svm_model</b> parameter in the command line or the ini file. This file should have been produced by the <a class="el" href="TOPP_RTModel.html">RTModel</a> application. <br/>
For retention time prediction the peptide sequences are extracted from the idXML inputfile and passed to the svm. The svm then predicts retention times according to the trained model. The predicted retention times are stored as</p>
<div class="fragment"><div class="line"><userParam name=<span class="stringliteral">"predicted_retention_time"</span> value=<span class="stringliteral">"<predicted retention time>"</span> /></div>
</div><!-- fragment --><p> inside the peptide entities in the idXML output file.</p>
<p>For separation prediction you have to specify two output file names. 'out_id:positive' is the filename of the peptides which are predicted to be collected by the column and 'out_id:negative' is the file of the predicted flowthrough peptides.</p>
<p>Retention time prediction and separation prediction cannot be combined!</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
RTPredict -- Predicts retention times for peptides using a model trained by RTModel.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
RTPredict <options>
Options (mandatory options marked with '*'):
-in_id <file> Peptides with precursor information (valid formats: 'idXML')
-in_text <file> Peptides as text-based file (valid formats: 'txt')
Output files in idXML format:
-out_id:file <file> Output file with peptide RT prediction (valid formats: 'idXML')
-out_id:positive <file> Output file in idXML format containing positive predictions (peptide separatio
n prediction - requires negative file to be present as well)
(valid formats: 'idXML')
-out_id:negative <file> Output file in idXML format containing negative predictions (peptide separatio
n prediction - requires positive file to be present as well)
(valid formats: 'idXML')
Output files in text format:
-out_text:file <file> Output file with predicted RT values (valid formats: 'csv')
-svm_model <file>* Svm model in libsvm format (can be produced by RTModel) (valid formats: 'txt')
-total_gradient_time <time> The time (in seconds) of the gradient (peptide RT prediction) (default: '1'
min: '1e-05')
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)
</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">+RTPredict</span><span class="node_description">Predicts retention times for peptides using a model trained by RTModel.</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 'RTPredict'</span></div>
<div class="item"><span class="item_name" style="padding-left:24px;">in_id</span><span class="item_value"></span>
<span class="item_description">peptides with precursor information</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;">in_text</span><span class="item_value"></span>
<span class="item_description">peptides as text-based file</span><span class="item_tags">input file</span><span class="item_restrictions">*.txt</span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">svm_model</span><span class="item_value"></span>
<span class="item_description">svm model in libsvm format (can be produced by RTModel)</span><span class="item_tags">input file</span><span class="item_restrictions">*.txt</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">total_gradient_time</span><span class="item_value">1</span>
<span class="item_description">the time (in seconds) of the gradient (peptide RT prediction)</span><span class="item_tags"></span><span class="item_restrictions">1e-05:∞</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">max_number_of_peptides</span><span class="item_value">100000</span>
<span class="item_description">the maximum number of peptides considered at once (bigger number will lead to faster results but needs more memory).<br></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;">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">+++out_id</span><span class="node_description">Output files in idXML format</span></div>
<div class="item"><span class="item_name" style="padding-left:32px;">file</span><span class="item_value"></span>
<span class="item_description">Output file with peptide RT prediction</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:32px;">positive</span><span class="item_value"></span>
<span class="item_description">Output file in idXML format containing positive predictions (peptide separation prediction - requires negative file to be present as well)<br></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:32px;">negative</span><span class="item_value"></span>
<span class="item_description">Output file in idXML format containing negative predictions (peptide separation prediction - requires positive file to be present as well)<br></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:32px;">rewrite_peptideidentification_rtmz</span><span class="item_value">false</span>
<span class="item_description">rewrites each peptideidentification's rt and mz from prediction and calculation (according to the best hit)</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="node"><span class="node_name">+++out_text</span><span class="node_description">Output files in text format</span></div>
<div class="item"><span class="item_name" style="padding-left:32px;">file</span><span class="item_value"></span>
<span class="item_description">Output file with predicted RT values</span><span class="item_tags">output file</span><span class="item_restrictions">*.csv</span></div></div>
<dl class="todo"><dt><b><a class="el" href="todo.html#_todo000035">Todo:</a></b></dt><dd>This need serious clean up! Combining certain input and output options will result in strange behaviour, especially when using text output/input. </dd></dl>
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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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