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<div class="title">MapRTTransformer </div> </div>
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<div class="textblock"><p>Applies retention time transformations to maps.</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 $" src="form_91.png"/> MapRTTransformer <img class="formulaInl" alt="$ \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_MapAlignerIdentification.html">MapAlignerIdentification</a> <br/>
(or another alignment 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 can apply retention time transformations to different types of data (mzML, featureXML, consensusXML, and idXML files). The transformations might have been generated by a previous invocation of one of the MapAligner tools (linked below). However, the trafoXML file format is not very complicated, so it is relatively easy to write (or generate) your own files. Each input file will give rise to one output file.</p>
<dl class="section see"><dt>See Also</dt><dd><a class="el" href="TOPP_MapAlignerIdentification.html">MapAlignerIdentification</a> <a class="el" href="TOPP_MapAlignerPoseClustering.html">MapAlignerPoseClustering</a> <a class="el" href="TOPP_MapAlignerSpectrum.html">MapAlignerSpectrum</a></dd></dl>
<p>With this tool it is also possible to invert transformations, or to fit a different model than originally specified to the retention time data in the transformation files. To fit a new model, choose a value other than "none" for the model type (see below).</p>
<p>Since OpenMS 1.8, the extraction of data for the alignment has been separate from the modeling of RT transformations based on that data. It is now possible to use different models independently of the chosen algorithm. The different available models are:</p>
<ul>
<li><a class="el" href="classOpenMS_1_1TransformationModelLinear.html">linear</a>: Linear model.</li>
<li><a class="el" href="classOpenMS_1_1TransformationModelBSpline.html">b_spline</a>: Smoothing spline (non-linear).</li>
<li><a class="el" href="classOpenMS_1_1TransformationModelInterpolated.html">interpolated</a>: Different types of interpolation.</li>
</ul>
<p>The following parameters control the modeling of RT transformations (they can be set in the "model" section of the INI file): <table border="1" style="border-style:solid; border-collapse:collapse; border-color:#c0c0c0;" width="100%" cellpadding="4">
<tr style="border-bottom:1px solid black; background:#fffff0"><th>Name</th><th>Type</th><th>Default</th><th>Restrictions</th><th>Description</th></tr>
<tr>
<td style="vertical-align:top"><b>type</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">none</td>
<td style="vertical-align:top">none, linear, b_spline, interpolated</td><td style="vertical-align:top">Type of model</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters for 'linear' model">linear</span>:symmetric_regression</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
<td style="vertical-align:top">true, false</td><td style="vertical-align:top">Perform linear regression on 'y - x' vs. 'y + x', instead of on 'y' vs. 'x'.</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters for 'b_spline' model">b_spline</span>:num_breakpoints</b></td>
<td style="vertical-align:top">int</td><td style="vertical-align:top">5</td>
<td style="vertical-align:top">min: 2</td><td style="vertical-align:top">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.</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters for 'b_spline' model">b_spline</span>:break_positions</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">uniform</td>
<td style="vertical-align:top">uniform, quantiles</td><td style="vertical-align:top">How to distribute the breakpoints on the retention time scale. 'uniform': intervals of equal size; 'quantiles': equal number of data points per interval.</td>
</tr>
<tr>
<td style="vertical-align:top"><b><span title="Parameters for 'interpolated' model">interpolated</span>:interpolation_type</b></td>
<td style="vertical-align:top">string</td><td style="vertical-align:top">cspline</td>
<td style="vertical-align:top">linear, cspline, akima</td><td style="vertical-align:top">Type of interpolation to apply.</td>
</tr>
</table>
<br/>
</p>
<dl class="section note"><dt>Note</dt><dd>As output options, either 'out' or 'trafo_out' has to be provided. They can be used together.</dd></dl>
<p><b>The command line parameters of this tool are:</b> <br/>
</p>
<pre class="fragment">
MapRTTransformer -- Applies retention time transformations to maps.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
MapRTTransformer <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 to transform (separated by blanks) (valid formats: 'mzML', 'featureXML',
'consensusXML', 'idXML')
-out <files> Output files separated by blanks. Either this option or 'trafo_out' have to be provided
. They can be used together. (valid formats: 'mzML', 'featureXML', 'consensusXML', 'idX
ML')
-trafo_in <files>* Transformations to apply (files separated by blanks) (valid formats: 'trafoXML')
-trafo_out <files> Transformation output files separated by blanks. Either this option or 'out' have to
be provided. They can be used together. (valid formats: 'trafoXML')
-invert Invert transformations (approximatively) before applying them
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:
- 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">+MapRTTransformer</span><span class="node_description">Applies retention time transformations to maps.</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 'MapRTTransformer'</span></div>
<div class="item"><span class="item_name" style="padding-left:24px;">in</span><span class="item_value">[]</span>
<span class="item_description">Input files to transform (separated by blanks)</span><span class="item_tags">input file</span><span class="item_restrictions">*.mzML,*.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 this option or 'trafo_out' have to be provided. They can be used together.</span><span class="item_tags">output file</span><span class="item_restrictions">*.mzML,*.featureXML,*.consensusXML,*.idXML</span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">trafo_in</span><span class="item_value">[]</span>
<span class="item_description">Transformations to apply (files separated by blanks)</span><span class="item_tags">input file</span><span class="item_restrictions">*.trafoXML</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 this option or 'out' have 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"><span class="item_name" style="padding-left:24px;">invert</span><span class="item_value">false</span>
<span class="item_description">Invert transformations (approximatively) before applying them</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">+++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">none</span>
<span class="item_description">Type of model</span><span class="item_tags"></span><span class="item_restrictions">none,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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