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<div class="title">FeatureLinkerLabeled </div> </div>
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<div class="textblock"><p>Groups corresponding isotope-labeled features in a feature map.</p>
<center> <table class="doxtable">
<tr>
<td align="center" bgcolor="#EBEBEB">potential predecessor tools </td><td valign="middle" rowspan="3"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> FeatureLinkerLabeled <img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> </td><td align="center" bgcolor="#EBEBEB">potential successor tools </td></tr>
<tr>
<td valign="middle" align="center" rowspan="2"><a class="el" href="TOPP_FeatureFinderCentroided.html">FeatureFinderCentroided</a> <br/>
(or another feature detection algorithm) </td><td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_ProteinQuantifier.html">ProteinQuantifier</a> </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_TextExporter.html">TextExporter</a> </td></tr>
</table>
</center><p>This tool provides an algorithm for grouping corresponding features in isotope-labeled experiments. For more details and algorithm-specific parameters (set in the ini file) see "Detailed Description" in the <a class="el" href="classOpenMS_1_1FeatureGroupingAlgorithmLabeled.html">algorithm documentation</a>.</p>
<p>FeatureLinkerLabeled takes one feature map (featureXML file) and stores the corresponding features in a consensus map (consensusXML file). Feature maps can be created from MS experiments (peak data) using one of the FeatureFinder TOPP tools.</p>
<dl class="section see"><dt>See Also</dt><dd><a class="el" href="TOPP_FeatureLinkerUnlabeled.html">FeatureLinkerUnlabeled</a> <a class="el" href="TOPP_FeatureLinkerUnlabeledQT.html">FeatureLinkerUnlabeledQT</a></dd></dl>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
FeatureLinkerLabeled -- Groups corresponding isotope-labeled features in a feature map.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
FeatureLinkerLabeled <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: 'featureXML')
-out <file>* Output file (valid formats: 'consensusXML')
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 Algorithm parameters 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">+FeatureLinkerLabeled</span><span class="node_description">Groups corresponding isotope-labeled features in a feature map.</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 'FeatureLinkerLabeled'</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">*.featureXML</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">*.consensusXML</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">Algorithm parameters section</span></div>
<div class="item"><span class="item_name" style="padding-left:32px;">rt_estimate</span><span class="item_value">true</span>
<span class="item_description">If 'true' the optimal RT pair distance and deviation are estimated by fitting a gaussian distribution to the histogram of pair distance. Note that this works only datasets with a significant amount of pairs! If 'false' the parameters 'rt_pair_dist', 'rt_dev_low' and 'rt_dev_high' define the optimal distance.</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;">rt_pair_dist</span><span class="item_value">-20</span>
<span class="item_description">optimal pair distance in RT [sec] from light to heavy feature</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">rt_dev_low</span><span class="item_value">15</span>
<span class="item_description">maximum allowed deviation below optimal retention time distance</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">rt_dev_high</span><span class="item_value">15</span>
<span class="item_description">maximum allowed deviation above optimal retention time distance</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">mz_pair_dists</span><span class="item_value">[4]</span>
<span class="item_description">optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3, .. by division through charge)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">mz_dev</span><span class="item_value">0.05</span>
<span class="item_description">maximum allowed deviation from optimal m/z distance<br></span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">mrm</span><span class="item_value">false</span>
<span class="item_description">this option should be used if the features correspond mrm chromatograms (additionally the precursor is taken into account)</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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