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<div class="title">MapAlignerPoseClustering </div> </div>
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<div class="textblock"><p>Corrects retention time distortions between maps, using a pose clustering approach.</p>
<center> <table class="doxtable">
<tr>
<td align="center" bgcolor="#EBEBEB">potential predecessor tools </td><td valign="middle" rowspan="2"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> MapAlignerPoseClustering <img class="formulaInl" alt="$ \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_FeatureFinderCentroided.html">FeatureFinderCentroided</a> <br/>
(or another feature finding algorithm) </td><td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_FeatureLinkerUnlabeled.html">FeatureLinkerUnlabeled</a> or <br/>
<a class="el" href="TOPP_FeatureLinkerUnlabeledQT.html">FeatureLinkerUnlabeledQT</a> </td></tr>
</table>
</center><p>This tool provides an algorithm to align the retention time scales of multiple input files, correcting shifts and distortions between them. Retention time adjustment may be necessary to correct for chromatography differences e.g. before data from multiple LC-MS runs can be combined (feature grouping), or when one run should be annotated with peptide identifications obtained in a different run.</p>
<p>All map alignment tools (MapAligner...) collect retention time data from the input files and - by fitting a model to this data</p>
<ul>
<li>compute transformations that map all runs to a common retention time scale. They can apply the transformations right away and return output files with aligned time scales (parameter <code>out</code>), and/or return descriptions of the transformations in trafoXML format (parameter <code>trafo_out</code>). Transformations stored as trafoXML can be applied to arbitrary files with the <a class="el" href="TOPP_MapRTTransformer.html">MapRTTransformer</a> tool.</li>
</ul>
<p>The map alignment tools differ in how they obtain retention time data for the modeling of transformations, and consequently what types of data they can be applied to. The alignment algorithm implemented here is the pose clustering algorithm as described in doi:10.1093/bioinformatics/btm209. It is used to find an affine transformation, which is further refined by a feature grouping step. This algorithm can be applied to features (featureXML) and peaks (mzML), but it has mostly been developed and tested on features. For more details and algorithm-specific parameters (set in the INI file) see "Detailed Description" in the <a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmPoseClustering.html">algorithm documentation</a>.</p>
<dl class="section see"><dt>See Also</dt><dd><a class="el" href="TOPP_MapAlignerPoseClustering.html">MapAlignerPoseClustering</a> <a class="el" href="TOPP_MapAlignerSpectrum.html">MapAlignerSpectrum</a> <a class="el" href="TOPP_MapRTTransformer.html">MapRTTransformer</a></dd></dl>
<p>This algorithm uses an affine transformation model.</p>
<p>To speed up the alignment, consider reducing 'max_number_of_peaks_considered'. If your alignment is not good enough, consider increasing this number (the alignment will take longer though).</p>
<p><b>The command line parameters of this tool are:</b> <br/>
</p>
<pre class="fragment">
MapAlignerIdentification -- Corrects retention time distortions between maps based on common peptide identifi
cations.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
MapAlignerIdentification <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 <files>* Input files separated by blanks (all must have the same file type) (valid format
s: 'featureXML', 'consensusXML', 'idXML')
-out <files> Output files separated by blanks. Either 'out' or 'trafo_out' has to be provided
. They can be used together. (valid formats: 'featureXML', 'consensusXML', 'idXM
L')
-trafo_out <files> Transformation output files separated by blanks. Either 'out' or 'trafo_out'
has to be provided. They can be used together. (valid formats: 'trafoXML')
Options to define a reference file (use either 'file' or 'index', not both; if neither is given 'index' is
used).:
-reference:file <file> File to use as reference (same file format as input files required) (valid forma
ts: 'featureXML', 'consensusXML', 'idXML')
-reference:index <number> Use one of the input files as reference ('1' for the first file, etc.).
If '0', no explicit reference is set - the algorithm will select a reference. (
default: '0' min: '0')
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
- model Options to control the modeling of retention time transformations from data
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">+MapAlignerIdentification</span><span class="node_description">Corrects retention time distortions between maps based on common peptide identifications.</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 'MapAlignerIdentification'</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 files separated by blanks (all must have the same file type)</span><span class="item_tags">input file</span><span class="item_restrictions">*.featureXML,*.consensusXML,*.idXML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">out</span><span class="item_value">[]</span>
<span class="item_description">Output files separated by blanks. Either 'out' or 'trafo_out' has to be provided. They can be used together.</span><span class="item_tags">output file</span><span class="item_restrictions">*.featureXML,*.consensusXML,*.idXML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">trafo_out</span><span class="item_value">[]</span>
<span class="item_description">Transformation output files separated by blanks. Either 'out' or 'trafo_out' has to be provided. They can be used together.</span><span class="item_tags">output file</span><span class="item_restrictions">*.trafoXML</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">+++reference</span><span class="node_description">Options to define a reference file (use either 'file' or 'index', not both; if neither is given 'index' is used).</span></div>
<div class="item"><span class="item_name" style="padding-left:32px;">file</span><span class="item_value"></span>
<span class="item_description">File to use as reference (same file format as input files required)</span><span class="item_tags">input file</span><span class="item_restrictions">*.featureXML,*.consensusXML,*.idXML</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">index</span><span class="item_value">0</span>
<span class="item_description">Use one of the input files as reference ('1' for the first file, etc.).<br>If '0', no explicit reference is set - the algorithm will select a reference.</span><span class="item_tags"></span><span class="item_restrictions">0:∞</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;">peptide_score_threshold</span><span class="item_value">0</span>
<span class="item_description">Score threshold for peptide hits to be used in the alignment.<br>Select a value that allows only 'high confidence' matches.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:32px;">min_run_occur</span><span class="item_value">2</span>
<span class="item_description">Minimum number of runs (incl. reference, if any) a peptide must occur in to be used for the alignment.<br>Unless you have very few runs or identifications, increase this value to focus on more informative peptides.</span><span class="item_tags"></span><span class="item_restrictions">2:∞</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">max_rt_shift</span><span class="item_value">0.5</span>
<span class="item_description">Maximum realistic RT difference for a peptide (median per run vs. reference). Peptides with higher shifts (outliers) are not used to compute the alignment.<br>If 0, no limit (disable filter); if > 1, the final value in seconds; if <= 1, taken as a fraction of the range of the reference RT scale.</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">use_unassigned_peptides</span><span class="item_value">true</span>
<span class="item_description">Should unassigned peptide identifications be used when computing an alignment of feature maps? If 'false', only peptide IDs assigned to features will be used.</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_feature_rt</span><span class="item_value">false</span>
<span class="item_description">When aligning feature maps, don't use the retention time of a peptide identification directly; instead, use the retention time of the centroid of the feature (apex of the elution profile) that the peptide was matched to. If different identifications are matched to one feature, only the peptide closest to the centroid in RT is used.<br>Precludes 'use_unassigned_peptides'.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="node"><span class="node_name">+++model</span><span class="node_description">Options to control the modeling of retention time transformations from data</span></div>
<div class="item"><span class="item_name" style="padding-left:32px;">type</span><span class="item_value">b_spline</span>
<span class="item_description">Type of model</span><span class="item_tags"></span><span class="item_restrictions">linear,b_spline,interpolated</span></div> <div class="node"><span class="node_name">++++linear</span><span class="node_description">Parameters for 'linear' model</span></div>
<div class="item"><span class="item_name" style="padding-left:40px;">symmetric_regression</span><span class="item_value">false</span>
<span class="item_description">Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="node"><span class="node_name">++++b_spline</span><span class="node_description">Parameters for 'b_spline' model</span></div>
<div class="item"><span class="item_name" style="padding-left:40px;">num_breakpoints</span><span class="item_value">5</span>
<span class="item_description">Number of breakpoints of the cubic spline in the smoothing step. More breakpoints mean less smoothing. Reduce this number if the transformation has an unexpected shape.</span><span class="item_tags"></span><span class="item_restrictions">2:∞</span></div> <div class="item"><span class="item_name" style="padding-left:40px;">break_positions</span><span class="item_value">uniform</span>
<span class="item_description">How to distribute the breakpoints on the retention time scale. 'uniform': intervals of equal size; 'quantiles': equal number of data points per interval.</span><span class="item_tags"></span><span class="item_restrictions">uniform,quantiles</span></div> <div class="node"><span class="node_name">++++interpolated</span><span class="node_description">Parameters for 'interpolated' model</span></div>
<div class="item"><span class="item_name" style="padding-left:40px;">interpolation_type</span><span class="item_value">cspline</span>
<span class="item_description">Type of interpolation to apply.</span><span class="item_tags"></span><span class="item_restrictions">linear,cspline,akima</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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