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<div class="title">FeatureFinderIsotopeWavelet </div> </div>
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<div class="textblock"><p>The feature detection application for quantitation.</p>
<center> <table class="doxtable">
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<td align="center" bgcolor="#EBEBEB" rowspan="1">pot. predecessor tools </td><td valign="middle" rowspan="3"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> FeatureFinderIsotopeWavelet <img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> </td><td align="center" bgcolor="#EBEBEB">pot. successor tools </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_NoiseFilterSGolay.html">NoiseFilterSGolay</a> </td><td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_MapAlignerPoseClustering.html">MapAlignerPoseClustering</a> <br/>
(or another alignment tool) </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_NoiseFilterGaussian.html">NoiseFilterGaussian</a> </td><td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_FeatureLinkerUnlabeled.html">FeatureLinkerUnlabeled</a> <br/>
(or another feature grouping tool) </td></tr>
</table>
</center><p>This module identifies "features" in a LC/MS map. By feature, we understand a peptide in a MS sample that reveals a characteristic isotope distribution. The algorithm computes positions in rt and m/z dimension and a charge estimate of each peptide.</p>
<p>The algorithm identifies pronounced regions of the data around so-called <code>seeds</code>. In the next step, we iteratively fit a model of the isotope profile and the retention time to these data points. Data points with a low probability under this model are removed from the feature region. The intensity of the feature is then given by the sum of the data points included in its regions.</p>
<p>How to find suitable parameters and details of the different algorithms implemented are described in the <a class="el" href="TOPP_example_featuredetection.html">TOPP tutorial</a>.</p>
<dl class="section note"><dt>Note</dt><dd>that the wavelet transform is very slow on high-resolution spectra (i.e. FT, Orbitrap). We recommend to use a noise or intensity filter to remove spurious points first and to speed-up the feature detection process.</dd></dl>
<p>Specialized tools are available for some experimental techniques: <a class="el" href="TOPP_SILACAnalyzer.html">SILACAnalyzer</a>, <a class="el" href="TOPP_ITRAQAnalyzer.html">ITRAQAnalyzer</a>.</p>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
FeatureFinderIsotopeWavelet -- Detects two-dimensional features in LC-MS data.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
FeatureFinderIsotopeWavelet <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: 'mzML')
-out <file>* Output file (valid formats: 'featureXML')
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 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">+FeatureFinderIsotopeWavelet</span><span class="node_description">Detects two-dimensional features in LC-MS data.</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 'FeatureFinderIsotopeWavelet'</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">*.mzML</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">*.featureXML</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 section</span></div>
<div class="item"><span class="item_name" style="padding-left:32px;">max_charge</span><span class="item_value">3</span>
<span class="item_description">The maximal charge state to be considered.</span><span class="item_tags"></span><span class="item_restrictions">1:∞</span></div> <div class="item"><span class="item_name" style="padding-left:32px;">intensity_threshold</span><span class="item_value">-1</span>
<span class="item_description">The final threshold t' is build upon the formula: t' = av+t*sd, where t is the intensity_threshold, av the average intensity within the wavelet transformed signal and sd the standard deviation of the transform. If you set intensity_threshold=-1, t' will be zero.<br>As the 'optimal' value for this parameter is highly data dependent, we would recommend to start with -1, which will also extract features with very low signal-to-noise ratio. Subsequently, one might increase the threshold to find an optimized trade-off between false positives and true positives. Depending on the dynamic range of your spectra, suitable value ranges include: -1, [0:10], and if your data features even very high intensity values, t can also adopt values up to around 30. Please note that this parameter is not of an integer type, s.t. you can also use t:=0.1, e.g.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">intensity_type</span><span class="item_value">ref</span>
<span class="item_description">Determines the intensity type returned for the identified features. 'ref' (default) returns the sum of the intensities of each isotopic peak within an isotope pattern. 'trans' refers to the intensity of the monoisotopic peak within the wavelet transform. 'corrected' refers also to the transformed intensity with an attempt to remove the effects of the convolution. While the latter ones might be preferable for qualitative analyses, 'ref' might be the best option to obtain quantitative results. Please note that intensity values might be spoiled (in particular for the option 'ref'), as soon as patterns overlap (see also the explanations given in the class documentation of FeatureFinderAlgorihtmIsotopeWavelet).</span><span class="item_tags"></span><span class="item_restrictions">ref,trans,corrected</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:32px;">check_ppm</span><span class="item_value">false</span>
<span class="item_description">Enables/disables a ppm test vs. the averagine model, i.e. potential peptide masses are checked for plausibility. In addition, a heuristic correcting potential mass shifts induced by the wavelet is applied.</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;">hr_data</span><span class="item_value">false</span>
<span class="item_description">Must be true in case of high-resolution data, i.e. for spectra featuring large m/z-gaps (present in FTICR and Orbitrap data, e.g.). Please check a single MS scan out of your recording, if you are unsure.</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="node"><span class="node_name">++++sweep_line</span><span class="node_description"></span></div>
<div class="item item_advanced"><span class="item_name" style="padding-left:40px;">rt_votes_cutoff</span><span class="item_value">5</span>
<span class="item_description">Defines the minimum number of subsequent scans where a pattern must occur to be considered as a feature.</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:40px;">rt_interleave</span><span class="item_value">1</span>
<span class="item_description">Defines the maximum number of scans (w.r.t. rt_votes_cutoff) where an expected pattern is missing. There is usually no reason to change the default value.</span><span class="item_tags"></span><span class="item_restrictions">0:∞</span></div></div>
<p>For the parameters of the algorithm section see the algorithms documentation: <br/>
<a class="el" href="classOpenMS_1_1FeatureFinderAlgorithmIsotopeWavelet.html">isotope_wavelet</a> <br/>
</p>
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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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