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<li class="navelem"><a class="el" href="namespaceOpenMS.html">OpenMS</a></li><li class="navelem"><a class="el" href="classOpenMS_1_1IsobaricNormalizer.html">IsobaricNormalizer</a></li> </ul>
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<p>Performs median normalization on the extracted ratios of isobaric labeling experiment.
<a href="classOpenMS_1_1IsobaricNormalizer.html#details">More...</a></p>
<p><code>#include <<a class="el" href="IsobaricNormalizer_8h_source.html">OpenMS/ANALYSIS/QUANTITATION/IsobaricNormalizer.h</a>></code></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr class="memitem:adf7688e922b629e48bdfdd3a1ec5d56c"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1IsobaricNormalizer.html#adf7688e922b629e48bdfdd3a1ec5d56c">IsobaricNormalizer</a> (const <a class="el" href="classOpenMS_1_1IsobaricQuantitationMethod.html">IsobaricQuantitationMethod</a> *const quant_method)</td></tr>
<tr class="memdesc:adf7688e922b629e48bdfdd3a1ec5d56c"><td class="mdescLeft"> </td><td class="mdescRight">Default c'tor. <a href="#adf7688e922b629e48bdfdd3a1ec5d56c">More...</a><br/></td></tr>
<tr class="separator:adf7688e922b629e48bdfdd3a1ec5d56c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:adb0032e7b1184031d2146b1648572844"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1IsobaricNormalizer.html#adb0032e7b1184031d2146b1648572844">IsobaricNormalizer</a> (const <a class="el" href="classOpenMS_1_1IsobaricNormalizer.html">IsobaricNormalizer</a> &other)</td></tr>
<tr class="memdesc:adb0032e7b1184031d2146b1648572844"><td class="mdescLeft"> </td><td class="mdescRight">Copy c'tor. <a href="#adb0032e7b1184031d2146b1648572844">More...</a><br/></td></tr>
<tr class="separator:adb0032e7b1184031d2146b1648572844"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a719bd11c0b1e71980d93b7b506e4fb99"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1IsobaricNormalizer.html">IsobaricNormalizer</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1IsobaricNormalizer.html#a719bd11c0b1e71980d93b7b506e4fb99">operator=</a> (const <a class="el" href="classOpenMS_1_1IsobaricNormalizer.html">IsobaricNormalizer</a> &rhs)</td></tr>
<tr class="memdesc:a719bd11c0b1e71980d93b7b506e4fb99"><td class="mdescLeft"> </td><td class="mdescRight">Assignment operator. <a href="#a719bd11c0b1e71980d93b7b506e4fb99">More...</a><br/></td></tr>
<tr class="separator:a719bd11c0b1e71980d93b7b506e4fb99"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5b1a0a2a900be3e741f036df2e828289"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1IsobaricNormalizer.html#a5b1a0a2a900be3e741f036df2e828289">normalize</a> (<a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &consensus_map)</td></tr>
<tr class="memdesc:a5b1a0a2a900be3e741f036df2e828289"><td class="mdescLeft"> </td><td class="mdescRight">Normalizes the intensity ratios in the given input map (using median). <a href="#a5b1a0a2a900be3e741f036df2e828289">More...</a><br/></td></tr>
<tr class="separator:a5b1a0a2a900be3e741f036df2e828289"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-methods"></a>
Private Member Functions</h2></td></tr>
<tr class="memitem:a477b7a6ab263fca74225b6718c828b70"><td class="memItemLeft" align="right" valign="top">ConsensusFeature::HandleSetType::iterator </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1IsobaricNormalizer.html#a477b7a6ab263fca74225b6718c828b70">findReferenceChannel_</a> (<a class="el" href="classOpenMS_1_1ConsensusFeature.html">ConsensusFeature</a> &cf, const <a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &consensus_map) const </td></tr>
<tr class="memdesc:a477b7a6ab263fca74225b6718c828b70"><td class="mdescLeft"> </td><td class="mdescRight">Given a <a class="el" href="classOpenMS_1_1ConsensusFeature.html" title="A 2-dimensional consensus feature. ">ConsensusFeature</a> the method will return an iterator pointing to the consensus element representing the reference channel. <a href="#a477b7a6ab263fca74225b6718c828b70">More...</a><br/></td></tr>
<tr class="separator:a477b7a6ab263fca74225b6718c828b70"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a12cbec4a7e310de12139116583f0363e"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1IsobaricNormalizer.html#a12cbec4a7e310de12139116583f0363e">buildVectorIndex_</a> (const <a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> &consensus_map)</td></tr>
<tr class="memdesc:a12cbec4a7e310de12139116583f0363e"><td class="mdescLeft"> </td><td class="mdescRight">Constructs a mapping from file description to the index in the corresponding ratio/intensity vectors. <a href="#a12cbec4a7e310de12139116583f0363e">More...</a><br/></td></tr>
<tr class="separator:a12cbec4a7e310de12139116583f0363e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a20af01a77b3f2d2f980f4382abf102f8"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1IsobaricNormalizer.html#a20af01a77b3f2d2f980f4382abf102f8">collectRatios_</a> (const <a class="el" href="classOpenMS_1_1ConsensusFeature.html">ConsensusFeature</a> &cf, const <a class="el" href="classOpenMS_1_1Peak2D.html#a4a8c5b2adc05e9ff96a007385bfe9b47">Peak2D::IntensityType</a> &ref_intensity)</td></tr>
<tr class="memdesc:a20af01a77b3f2d2f980f4382abf102f8"><td class="mdescLeft"> </td><td class="mdescRight">Collects ratios and intensities for a given <a class="el" href="classOpenMS_1_1ConsensusFeature.html" title="A 2-dimensional consensus feature. ">ConsensusFeature</a>. <a href="#a20af01a77b3f2d2f980f4382abf102f8">More...</a><br/></td></tr>
<tr class="separator:a20af01a77b3f2d2f980f4382abf102f8"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a44eba9c65b194d56da4fed1ec4d73e2e"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1IsobaricNormalizer.html#a44eba9c65b194d56da4fed1ec4d73e2e">computeNormalizationFactors_</a> (std::vector< <a class="el" href="classOpenMS_1_1Peak2D.html#a4a8c5b2adc05e9ff96a007385bfe9b47">Peak2D::IntensityType</a> > &normalization_factors)</td></tr>
<tr class="memdesc:a44eba9c65b194d56da4fed1ec4d73e2e"><td class="mdescLeft"> </td><td class="mdescRight">Computes the normalization factors from the given peptide ratios. <a href="#a44eba9c65b194d56da4fed1ec4d73e2e">More...</a><br/></td></tr>
<tr class="separator:a44eba9c65b194d56da4fed1ec4d73e2e"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-attribs"></a>
Private Attributes</h2></td></tr>
<tr class="memitem:aff3698fe9659f86c499ca3c76ab72dfe"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1IsobaricQuantitationMethod.html">IsobaricQuantitationMethod</a> * </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1IsobaricNormalizer.html#aff3698fe9659f86c499ca3c76ab72dfe">quant_meth_</a></td></tr>
<tr class="memdesc:aff3698fe9659f86c499ca3c76ab72dfe"><td class="mdescLeft"> </td><td class="mdescRight">The selected quantitation method that will be used for the normalization. <a href="#aff3698fe9659f86c499ca3c76ab72dfe">More...</a><br/></td></tr>
<tr class="separator:aff3698fe9659f86c499ca3c76ab72dfe"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a9bfdeef5c9747d8394796dc0fdefe618"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1IsobaricNormalizer.html#a9bfdeef5c9747d8394796dc0fdefe618">reference_channel_name_</a></td></tr>
<tr class="memdesc:a9bfdeef5c9747d8394796dc0fdefe618"><td class="mdescLeft"> </td><td class="mdescRight">The name of the reference channel as given in the IsobaricChannelInformation. <a href="#a9bfdeef5c9747d8394796dc0fdefe618">More...</a><br/></td></tr>
<tr class="separator:a9bfdeef5c9747d8394796dc0fdefe618"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a3759cb8db64e5c780451e598fa933029"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Map.html">Map</a>< <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1IsobaricNormalizer.html#a3759cb8db64e5c780451e598fa933029">map_to_vec_index_</a></td></tr>
<tr class="memdesc:a3759cb8db64e5c780451e598fa933029"><td class="mdescLeft"> </td><td class="mdescRight">The mapping between map indices and the corresponding indices in the peptide ratio/intensity vectors. <a href="#a3759cb8db64e5c780451e598fa933029">More...</a><br/></td></tr>
<tr class="separator:a3759cb8db64e5c780451e598fa933029"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a899ad5d48301da6b0dcc4be09d5cf21e"><td class="memItemLeft" align="right" valign="top"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1IsobaricNormalizer.html#a899ad5d48301da6b0dcc4be09d5cf21e">ref_map_id_</a></td></tr>
<tr class="memdesc:a899ad5d48301da6b0dcc4be09d5cf21e"><td class="mdescLeft"> </td><td class="mdescRight">The index of the reference channel in the peptide ratio/intensity vectors. <a href="#a899ad5d48301da6b0dcc4be09d5cf21e">More...</a><br/></td></tr>
<tr class="separator:a899ad5d48301da6b0dcc4be09d5cf21e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ab768052c235798d6a4ffc079fb0a5eac"><td class="memItemLeft" align="right" valign="top">std::vector< std::vector<br class="typebreak"/>
< <a class="el" href="classOpenMS_1_1Peak2D.html#a4a8c5b2adc05e9ff96a007385bfe9b47">Peak2D::IntensityType</a> > > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1IsobaricNormalizer.html#ab768052c235798d6a4ffc079fb0a5eac">peptide_ratios_</a></td></tr>
<tr class="memdesc:ab768052c235798d6a4ffc079fb0a5eac"><td class="mdescLeft"> </td><td class="mdescRight">Collection containing the collected peptide ratios for the individual channels. <a href="#ab768052c235798d6a4ffc079fb0a5eac">More...</a><br/></td></tr>
<tr class="separator:ab768052c235798d6a4ffc079fb0a5eac"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af25c34a532a2dc7c80b99a8b94612d73"><td class="memItemLeft" align="right" valign="top">std::vector< std::vector<br class="typebreak"/>
< <a class="el" href="classOpenMS_1_1Peak2D.html#a4a8c5b2adc05e9ff96a007385bfe9b47">Peak2D::IntensityType</a> > > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1IsobaricNormalizer.html#af25c34a532a2dc7c80b99a8b94612d73">peptide_intensities_</a></td></tr>
<tr class="memdesc:af25c34a532a2dc7c80b99a8b94612d73"><td class="mdescLeft"> </td><td class="mdescRight">Collection containing the collected peptide intensities for the individual channels. <a href="#af25c34a532a2dc7c80b99a8b94612d73">More...</a><br/></td></tr>
<tr class="separator:af25c34a532a2dc7c80b99a8b94612d73"><td class="memSeparator" colspan="2"> </td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
<div class="textblock"><p>Performs median normalization on the extracted ratios of isobaric labeling experiment. </p>
</div><h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1IsobaricNormalizer.html">IsobaricNormalizer</a> </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1IsobaricQuantitationMethod.html">IsobaricQuantitationMethod</a> *const </td>
<td class="paramname"><em>quant_method</em></td><td>)</td>
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<p>Default c'tor. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1IsobaricNormalizer.html">IsobaricNormalizer</a> </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1IsobaricNormalizer.html">IsobaricNormalizer</a> & </td>
<td class="paramname"><em>other</em></td><td>)</td>
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<p>Copy c'tor. </p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname">void buildVectorIndex_ </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> & </td>
<td class="paramname"><em>consensus_map</em></td><td>)</td>
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<p>Constructs a mapping from file description to the index in the corresponding ratio/intensity vectors. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramname">consensus_map</td><td>The consensus map for which the mapping should be build. </td></tr>
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<td class="memname">void collectRatios_ </td>
<td>(</td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1ConsensusFeature.html">ConsensusFeature</a> & </td>
<td class="paramname"><em>cf</em>, </td>
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<td></td>
<td class="paramtype">const <a class="el" href="classOpenMS_1_1Peak2D.html#a4a8c5b2adc05e9ff96a007385bfe9b47">Peak2D::IntensityType</a> & </td>
<td class="paramname"><em>ref_intensity</em> </td>
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<td>)</td>
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<p>Collects ratios and intensities for a given <a class="el" href="classOpenMS_1_1ConsensusFeature.html" title="A 2-dimensional consensus feature. ">ConsensusFeature</a>. </p>
<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">cf</td><td>The consensus feature to evaluate. </td></tr>
<tr><td class="paramname">ref_intensity</td><td>The intensity of the reference channel. </td></tr>
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<td class="memname">void computeNormalizationFactors_ </td>
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<td class="paramtype">std::vector< <a class="el" href="classOpenMS_1_1Peak2D.html#a4a8c5b2adc05e9ff96a007385bfe9b47">Peak2D::IntensityType</a> > & </td>
<td class="paramname"><em>normalization_factors</em></td><td>)</td>
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<p>Computes the normalization factors from the given peptide ratios. </p>
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<tr><td class="paramname">normalization_factors</td><td>The normalization factors to compute. </td></tr>
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<td class="memname">ConsensusFeature::HandleSetType::iterator findReferenceChannel_ </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1ConsensusMap.html">ConsensusMap</a> & </td>
<td class="paramname"><em>consensus_map</em> </td>
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<p>Given a <a class="el" href="classOpenMS_1_1ConsensusFeature.html" title="A 2-dimensional consensus feature. ">ConsensusFeature</a> the method will return an iterator pointing to the consensus element representing the reference channel. </p>
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<tr><td class="paramname">cf</td><td>The <a class="el" href="classOpenMS_1_1ConsensusFeature.html" title="A 2-dimensional consensus feature. ">ConsensusFeature</a> for which the reference element should be found. </td></tr>
<tr><td class="paramname">consensus_map</td><td>The <a class="el" href="classOpenMS_1_1ConsensusMap.html" title="A container for consensus elements. ">ConsensusMap</a> in which the reference element should be found. </td></tr>
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<dl class="section return"><dt>Returns</dt><dd>An iterator pointing to the consensus element of the reference channel. <a class="el" href="classOpenMS_1_1ConsensusFeature.html#acad38d52497a975bfb6f2f6acd76631f">ConsensusFeature::end()</a> if the reference channel is not contained. </dd></dl>
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<td class="memname">void normalize </td>
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<p>Normalizes the intensity ratios in the given input map (using median). </p>
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<tr><td class="paramname">consensus_map</td><td>The map to normalize. </td></tr>
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<td class="memname"><a class="el" href="classOpenMS_1_1IsobaricNormalizer.html">IsobaricNormalizer</a>& operator= </td>
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<td class="paramname"><em>rhs</em></td><td>)</td>
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<p>Assignment operator. </p>
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<h2 class="groupheader">Member Data Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1Map.html">Map</a><<a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>, <a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a>> map_to_vec_index_</td>
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<p>The mapping between map indices and the corresponding indices in the peptide ratio/intensity vectors. </p>
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<td class="memname">std::vector<std::vector<<a class="el" href="classOpenMS_1_1Peak2D.html#a4a8c5b2adc05e9ff96a007385bfe9b47">Peak2D::IntensityType</a>> > peptide_intensities_</td>
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<p>Collection containing the collected peptide intensities for the individual channels. </p>
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<td class="memname">std::vector<std::vector<<a class="el" href="classOpenMS_1_1Peak2D.html#a4a8c5b2adc05e9ff96a007385bfe9b47">Peak2D::IntensityType</a>> > peptide_ratios_</td>
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<p>Collection containing the collected peptide ratios for the individual channels. </p>
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<td class="memname">const <a class="el" href="classOpenMS_1_1IsobaricQuantitationMethod.html">IsobaricQuantitationMethod</a>* quant_meth_</td>
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<p>The selected quantitation method that will be used for the normalization. </p>
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<td class="memname"><a class="el" href="group__Concept.html#gaf9ecec2d692138fab9167164a457cbd4">Size</a> ref_map_id_</td>
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<p>The index of the reference channel in the peptide ratio/intensity vectors. </p>
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<td class="memname"><a class="el" href="group__Concept.html#ga7cc214a236ad3bb6ad435bdcf5262a3f">Int</a> reference_channel_name_</td>
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<p>The name of the reference channel as given in the IsobaricChannelInformation. </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 11:19:27 using doxygen 1.8.5</font></TD>
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