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<div class="title">MapAlignerSpectrum </div> </div>
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<div class="textblock"><p>Corrects retention time distortions between maps by aligning spectra.</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 $" src="form_91.png"/> MapAlignerSpectrumAlignment <img class="formulaInl" alt="$ \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_FileConverter.html">FileConverter</a> </td><td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_FeatureFinderCentroided.html">FeatureFinderCentroided</a> <br/>
(or another feature finding algorithm) </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 - 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.</p>
<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. Here, an experimental algorithm based on spectrum alignment is implemented. It is only applicable to peak maps (mzML format). For more details and algorithm-specific parameters (set in the INI file) see "Detailed Description" in the <a class="el" href="classOpenMS_1_1MapAlignmentAlgorithmSpectrumAlignment.html">algorithm documentation</a>.</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_MapRTTransformer.html">MapRTTransformer</a></dd></dl>
<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. This algorithm has been tested mostly with the "interpolated" model. 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">interpolated</td>
<td style="vertical-align:top">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/>
<b>The command line parameters of this tool are:</b> <br/>
</p>
<pre class="fragment">
MapAlignerSpectrum -- Corrects retention time distortions between maps by spectrum alignment.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
MapAlignerSpectrum <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 formats: 'mzM
L')
-out <files> Output files separated by blanks. Either 'out' or 'trafo_out' has to be provided. They
can be used together. (valid formats: 'mzML')
-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')
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">+MapAlignerSpectrum</span><span class="node_description">Corrects retention time distortions between maps by spectrum alignment.</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 'MapAlignerSpectrum'</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">*.mzML</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">*.mzML</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">+++algorithm</span><span class="node_description">Algorithm parameters section</span></div>
<div class="item"><span class="item_name" style="padding-left:32px;">gapcost</span><span class="item_value">1</span>
<span class="item_description"> This Parameter stands for the cost of opining a gap in the Alignment. A Gap means that one Spectrum can not be aligned directly to another Spectrum in the Map. This happens, when the similarity of both spectra a too low or even not present. Imagen as a insert or delete of the spectrum in the map. The gap is necessary for aligning, if we open a gap there is a possibility that an another spectrum can be correct aligned with a higher score as before without gap. But to open a gap is a negative event and has to be punished a bit, so such only in case it 's a good choice to open a gap, if the score is bad enough. The Parameter is to giving as a positive number, the implementation convert it to a negative number.</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">affinegapcost</span><span class="item_value">0.5</span>
<span class="item_description"> This Parameter controls the cost of extension a already open gap. The idea behind the affine gapcost lies under the assumption, that it is better to get a long distance of connected gaps than to have a structure gap match gap match. There for the punishment for the extension of a gap has to be lower than the normal gapcost. If the the result of the aligmnet show high compression, it is a good idea to lower the affine gapcost or the normal gapcost.</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;">cutoff_score</span><span class="item_value">0.7</span>
<span class="item_description">The Parameter defines the threshold which filtered Spectra, these Spectra are high potential candidate for deciding the interval of a sub-alignment. Only those pair of Spectra are selected, which has a score higher or same of the threshold.</span><span class="item_tags"></span><span class="item_restrictions">0:1</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">bucketsize</span><span class="item_value">100</span>
<span class="item_description">Defines the numbers of buckets. It is a quantize of the interval of those points, which defines the main alignment(match points). These points have to filtered, to reduce the amount of points for the calculating a smoother spline curve.</span><span class="item_tags"></span><span class="item_restrictions">1:∞</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">anchorpoints</span><span class="item_value">100</span>
<span class="item_description">Defines the percent of numbers of match points which a selected from one bucket. The high score pairs are previously selected. The reduction of match points helps to get a smoother spline curve.</span><span class="item_tags"></span><span class="item_restrictions">1:100</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">debug</span><span class="item_value">false</span>
<span class="item_description">active the debug mode, there a files written starting with debug prefix.</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:32px;">mismatchscore</span><span class="item_value">-5</span>
<span class="item_description">Defines the score of two Spectra if they have no similarity to each other. </span><span class="item_tags"></span><span class="item_restrictions">-∞:0</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">scorefunction</span><span class="item_value">SteinScottImproveScore</span>
<span class="item_description"> The score function is the core of an alignment. The success of an alignment depends mostly of the elected score function. The score function return the similarity of two Spectrum back. The score influence defines later the way of possible traceback. There exist many way of algorithm to calculate the score.</span><span class="item_tags"></span><span class="item_restrictions">SteinScottImproveScore,ZhangSimilarityScore</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">interpolated</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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