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<TITLE>FalseDiscoveryRate Class Reference</TITLE>
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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_1FalseDiscoveryRate.html">FalseDiscoveryRate</a></li> </ul>
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<a href="#pub-methods">Public Member Functions</a> |
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<a href="#pri-methods">Private Member Functions</a> |
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<a href="classOpenMS_1_1FalseDiscoveryRate-members.html">List of all members</a> </div>
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<div class="title">FalseDiscoveryRate Class Reference<div class="ingroups"><a class="el" href="group__Analysis__ID.html">Identification</a></div></div> </div>
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<div class="contents">
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<p>Calculates an FDR from identifications.
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<a href="classOpenMS_1_1FalseDiscoveryRate.html#details">More...</a></p>
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<p><code>#include <<a class="el" href="FalseDiscoveryRate_8h_source.html">OpenMS/ANALYSIS/ID/FalseDiscoveryRate.h</a>></code></p>
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<div class="dynheader">
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Inheritance diagram for FalseDiscoveryRate:</div>
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<div class="dyncontent">
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<img src="classOpenMS_1_1FalseDiscoveryRate.png" usemap="#FalseDiscoveryRate_map" alt=""/>
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<map id="FalseDiscoveryRate_map" name="FalseDiscoveryRate_map">
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<area href="classOpenMS_1_1DefaultParamHandler.html" title="A base class for all classes handling default parameters. " alt="DefaultParamHandler" shape="rect" coords="0,0,133,24"/>
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<table class="memberdecls">
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-methods"></a>
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Public Member Functions</h2></td></tr>
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<tr class="memitem:a5337bdfee210c632a93341962a655caf"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FalseDiscoveryRate.html#a5337bdfee210c632a93341962a655caf">FalseDiscoveryRate</a> ()</td></tr>
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<tr class="memdesc:a5337bdfee210c632a93341962a655caf"><td class="mdescLeft"> </td><td class="mdescRight">Default constructor. <a href="#a5337bdfee210c632a93341962a655caf">More...</a><br/></td></tr>
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<tr class="separator:a5337bdfee210c632a93341962a655caf"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ade46bf920d0b8471b917a6cea2bed3e6"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FalseDiscoveryRate.html#ade46bf920d0b8471b917a6cea2bed3e6">apply</a> (std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > &fwd_ids, std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > &rev_ids)</td></tr>
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<tr class="memdesc:ade46bf920d0b8471b917a6cea2bed3e6"><td class="mdescLeft"> </td><td class="mdescRight">Calculates the FDR of two runs, a forward run and a decoy run on peptide level. <a href="#ade46bf920d0b8471b917a6cea2bed3e6">More...</a><br/></td></tr>
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<tr class="separator:ade46bf920d0b8471b917a6cea2bed3e6"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a84e469180436c079bf54addf9a619da3"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FalseDiscoveryRate.html#a84e469180436c079bf54addf9a619da3">apply</a> (std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > &id)</td></tr>
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<tr class="memdesc:a84e469180436c079bf54addf9a619da3"><td class="mdescLeft"> </td><td class="mdescRight">Calculates the FDR of one run from a concatenated sequence db search. <a href="#a84e469180436c079bf54addf9a619da3">More...</a><br/></td></tr>
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<tr class="separator:a84e469180436c079bf54addf9a619da3"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a3053e14a158f743ced2b792b6d9ab640"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FalseDiscoveryRate.html#a3053e14a158f743ced2b792b6d9ab640">apply</a> (std::vector< <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> > &fwd_ids, std::vector< <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> > &rev_ids)</td></tr>
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<tr class="memdesc:a3053e14a158f743ced2b792b6d9ab640"><td class="mdescLeft"> </td><td class="mdescRight">Calculates the FDR of two runs, a forward run and decoy run on protein level. <a href="#a3053e14a158f743ced2b792b6d9ab640">More...</a><br/></td></tr>
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<tr class="separator:a3053e14a158f743ced2b792b6d9ab640"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ab983877be843bfba1bd60b89b82b0369"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FalseDiscoveryRate.html#ab983877be843bfba1bd60b89b82b0369">apply</a> (std::vector< <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> > &ids)</td></tr>
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<tr class="memdesc:ab983877be843bfba1bd60b89b82b0369"><td class="mdescLeft"> </td><td class="mdescRight">Calculate the FDR of one run from a concatenated sequence db search. <a href="#ab983877be843bfba1bd60b89b82b0369">More...</a><br/></td></tr>
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<tr class="separator:ab983877be843bfba1bd60b89b82b0369"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="inherit_header pub_methods_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pub_methods_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/> Public Member Functions inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
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<tr class="memitem:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#afb6802fda161cb0c1a4a05597f94aecc">DefaultParamHandler</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &name)</td></tr>
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<tr class="memdesc:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Constructor with name that is displayed in error messages. <a href="#afb6802fda161cb0c1a4a05597f94aecc">More...</a><br/></td></tr>
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<tr class="separator:afb6802fda161cb0c1a4a05597f94aecc inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a954da7eef3cfddda446574eaadd20abb">DefaultParamHandler</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &rhs)</td></tr>
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<tr class="memdesc:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Copy constructor. <a href="#a954da7eef3cfddda446574eaadd20abb">More...</a><br/></td></tr>
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<tr class="separator:a954da7eef3cfddda446574eaadd20abb inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a11e9d6dd34fe8860874aa8abe0ec121b">~DefaultParamHandler</a> ()</td></tr>
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<tr class="memdesc:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Destructor. <a href="#a11e9d6dd34fe8860874aa8abe0ec121b">More...</a><br/></td></tr>
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<tr class="separator:a11e9d6dd34fe8860874aa8abe0ec121b inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ae6b6d68036a573a44f6609460ba2dfb6">operator=</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &rhs)</td></tr>
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<tr class="memdesc:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Assignment operator. <a href="#ae6b6d68036a573a44f6609460ba2dfb6">More...</a><br/></td></tr>
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<tr class="separator:ae6b6d68036a573a44f6609460ba2dfb6 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ac435f2dd4d9f9328db83af97129a8d7e">operator==</a> (const <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a> &rhs) const </td></tr>
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<tr class="memdesc:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Equality operator. <a href="#ac435f2dd4d9f9328db83af97129a8d7e">More...</a><br/></td></tr>
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<tr class="separator:ac435f2dd4d9f9328db83af97129a8d7e inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81">setParameters</a> (const <a class="el" href="classOpenMS_1_1Param.html">Param</a> &param)</td></tr>
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<tr class="memdesc:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Sets the parameters. <a href="#abc8067511cfc949ae942ea2b08588f81">More...</a><br/></td></tr>
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<tr class="separator:abc8067511cfc949ae942ea2b08588f81 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1Param.html">Param</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a7f6aab5a7dfbdd1c062a4352a29361f3">getParameters</a> () const </td></tr>
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<tr class="memdesc:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the parameters. <a href="#a7f6aab5a7dfbdd1c062a4352a29361f3">More...</a><br/></td></tr>
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<tr class="separator:a7f6aab5a7dfbdd1c062a4352a29361f3 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1Param.html">Param</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a02f02fa9832ca3e8d47c575a39803a2a">getDefaults</a> () const </td></tr>
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<tr class="memdesc:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the default parameters. <a href="#a02f02fa9832ca3e8d47c575a39803a2a">More...</a><br/></td></tr>
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<tr class="separator:a02f02fa9832ca3e8d47c575a39803a2a inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classOpenMS_1_1String.html">String</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#aaee0f2845288173de9f6ad47e6ad31d5">getName</a> () const </td></tr>
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<tr class="memdesc:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the name. <a href="#aaee0f2845288173de9f6ad47e6ad31d5">More...</a><br/></td></tr>
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<tr class="separator:aaee0f2845288173de9f6ad47e6ad31d5 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a77d37f2e1c12e8bd33ea0e660a89e927">setName</a> (const <a class="el" href="classOpenMS_1_1String.html">String</a> &name)</td></tr>
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<tr class="memdesc:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Mutable access to the name. <a href="#a77d37f2e1c12e8bd33ea0e660a89e927">More...</a><br/></td></tr>
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<tr class="separator:a77d37f2e1c12e8bd33ea0e660a89e927 inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">const std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a768d4a2093627a2f34728656a9721bdf">getSubsections</a> () const </td></tr>
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<tr class="memdesc:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Non-mutable access to the registered subsections. <a href="#a768d4a2093627a2f34728656a9721bdf">More...</a><br/></td></tr>
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<tr class="separator:a768d4a2093627a2f34728656a9721bdf inherit pub_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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</table><table class="memberdecls">
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pri-methods"></a>
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Private Member Functions</h2></td></tr>
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<tr class="memitem:a7856fd6f5eee4890faf125c4597c4e13"><td class="memItemLeft" align="right" valign="top"> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FalseDiscoveryRate.html#a7856fd6f5eee4890faf125c4597c4e13">FalseDiscoveryRate</a> (const <a class="el" href="classOpenMS_1_1FalseDiscoveryRate.html">FalseDiscoveryRate</a> &)</td></tr>
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<tr class="memdesc:a7856fd6f5eee4890faf125c4597c4e13"><td class="mdescLeft"> </td><td class="mdescRight">Not implemented. <a href="#a7856fd6f5eee4890faf125c4597c4e13">More...</a><br/></td></tr>
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<tr class="separator:a7856fd6f5eee4890faf125c4597c4e13"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a10c228d126879fe23dae71079429c6a4"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1FalseDiscoveryRate.html">FalseDiscoveryRate</a> & </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FalseDiscoveryRate.html#a10c228d126879fe23dae71079429c6a4">operator=</a> (const <a class="el" href="classOpenMS_1_1FalseDiscoveryRate.html">FalseDiscoveryRate</a> &)</td></tr>
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<tr class="memdesc:a10c228d126879fe23dae71079429c6a4"><td class="mdescLeft"> </td><td class="mdescRight">Not implemented. <a href="#a10c228d126879fe23dae71079429c6a4">More...</a><br/></td></tr>
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<tr class="separator:a10c228d126879fe23dae71079429c6a4"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:aa62b530f09b9276db563b40a4e862104"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1FalseDiscoveryRate.html#aa62b530f09b9276db563b40a4e862104">calculateFDRs_</a> (<a class="el" href="classOpenMS_1_1Map.html">Map</a>< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > &score_to_fdr, std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > &target_scores, std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > &decoy_scores, bool q_value, bool higher_score_better)</td></tr>
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<tr class="memdesc:aa62b530f09b9276db563b40a4e862104"><td class="mdescLeft"> </td><td class="mdescRight">calculates the fdr stored into fdrs, given two vectors of scores <a href="#aa62b530f09b9276db563b40a4e862104">More...</a><br/></td></tr>
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<tr class="separator:aa62b530f09b9276db563b40a4e862104"><td class="memSeparator" colspan="2"> </td></tr>
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</table><table class="memberdecls">
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<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="inherited"></a>
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Additional Inherited Members</h2></td></tr>
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<tr class="inherit_header pro_methods_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pro_methods_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/> Protected Member Functions inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
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<tr class="memitem:a776f7572fc4f466e9527ca233471920d inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">virtual void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a776f7572fc4f466e9527ca233471920d">updateMembers_</a> ()</td></tr>
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<tr class="memdesc:a776f7572fc4f466e9527ca233471920d inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">This method is used to update extra member variables at the end of the <a class="el" href="classOpenMS_1_1DefaultParamHandler.html#abc8067511cfc949ae942ea2b08588f81" title="Sets the parameters. ">setParameters()</a> method. <a href="#a776f7572fc4f466e9527ca233471920d">More...</a><br/></td></tr>
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<tr class="separator:a776f7572fc4f466e9527ca233471920d inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="memitem:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a2802c591e6d7fd3fd9cc35f5e875d0ba">defaultsToParam_</a> ()</td></tr>
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<tr class="memdesc:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Updates the parameters after the defaults have been set in the constructor. <a href="#a2802c591e6d7fd3fd9cc35f5e875d0ba">More...</a><br/></td></tr>
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<tr class="separator:a2802c591e6d7fd3fd9cc35f5e875d0ba inherit pro_methods_classOpenMS_1_1DefaultParamHandler"><td class="memSeparator" colspan="2"> </td></tr>
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<tr class="inherit_header pro_attribs_classOpenMS_1_1DefaultParamHandler"><td colspan="2" onclick="javascript:toggleInherit('pro_attribs_classOpenMS_1_1DefaultParamHandler')"><img src="closed.png" alt="-"/> Protected Attributes inherited from <a class="el" href="classOpenMS_1_1DefaultParamHandler.html">DefaultParamHandler</a></td></tr>
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<tr class="memitem:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Param.html">Param</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a28c73e623c63a4fe3bfceb1ae8274f39">param_</a></td></tr>
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<tr class="memdesc:a28c73e623c63a4fe3bfceb1ae8274f39 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for current parameters. <a href="#a28c73e623c63a4fe3bfceb1ae8274f39">More...</a><br/></td></tr>
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<tr class="memitem:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1Param.html">Param</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a761b1937850c141d0c6fff0e4d633a04">defaults_</a></td></tr>
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<tr class="memdesc:a761b1937850c141d0c6fff0e4d633a04 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for default parameters. This member should be filled in the constructor of derived classes! <a href="#a761b1937850c141d0c6fff0e4d633a04">More...</a><br/></td></tr>
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<tr class="memitem:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">std::vector< <a class="el" href="classOpenMS_1_1String.html">String</a> > </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#ac4b0e20bc59c7a5afe016c69067e428c">subsections_</a></td></tr>
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<tr class="memdesc:ac4b0e20bc59c7a5afe016c69067e428c inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Container for registered subsections. This member should be filled in the constructor of derived classes! <a href="#ac4b0e20bc59c7a5afe016c69067e428c">More...</a><br/></td></tr>
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<tr class="memitem:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top"><a class="el" href="classOpenMS_1_1String.html">String</a> </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a5a51f3f150b09068256195e934339a19">error_name_</a></td></tr>
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<tr class="memdesc:a5a51f3f150b09068256195e934339a19 inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">Name that is displayed in error messages during the parameter checking. <a href="#a5a51f3f150b09068256195e934339a19">More...</a><br/></td></tr>
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<tr class="memitem:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#a7c3b265b697a57615da5cd3274780efd">check_defaults_</a></td></tr>
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<tr class="memdesc:a7c3b265b697a57615da5cd3274780efd inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">If this member is set to false no checking if parameters in done;. <a href="#a7c3b265b697a57615da5cd3274780efd">More...</a><br/></td></tr>
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<tr class="memitem:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="classOpenMS_1_1DefaultParamHandler.html#aba444910e4fccb93f91bf7ab135f508a">warn_empty_defaults_</a></td></tr>
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<tr class="memdesc:aba444910e4fccb93f91bf7ab135f508a inherit pro_attribs_classOpenMS_1_1DefaultParamHandler"><td class="mdescLeft"> </td><td class="mdescRight">If this member is set to false no warning is emitted when defaults are empty;. <a href="#aba444910e4fccb93f91bf7ab135f508a">More...</a><br/></td></tr>
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<a name="details" id="details"></a><h2 class="groupheader">Detailed Description</h2>
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<div class="textblock"><p>Calculates an FDR from identifications. </p>
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<p>Either two runs of forward and decoy database identification or one run containing both (with marks) can be used to annotate each of the peptide hits with a FDR.</p>
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<p>Also q-values can be reported instead of p-values. q-values are basically only adjusted p-values, also ranging from 0 to 1, with lower values being preferable. When looking at the list of hits ordered by q-values, then a hit with q-value of <em>x</em> means that there is an <em>x*100</em> percent chance that all hits with a q-value <= <em>x</em> are a false positive hit.</p>
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<dl class="todo"><dt><b><a class="el" href="todo.html#_todo000001">Todo:</a></b></dt><dd>implement combined searches properly (Andreas) </dd></dl>
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<dl class="improvement"><dt><b><a class="el" href="improvement.html#_improvement000001">Improvement:</a></b></dt><dd>implement charge state separated fdr/q-values (Andreas)</dd></dl>
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<B>Parameters of this class are:</B><BR><BR>
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<table border="1" style="border-style:solid; border-collapse:collapse; border-color:#c0c0c0;" width="100%" cellpadding="4">
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<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>
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<td style="vertical-align:top"><b>q_value</b></td>
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<td style="vertical-align:top">string</td><td style="vertical-align:top">true</td>
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<td style="vertical-align:top">true, false</td><td style="vertical-align:top">If 'true', the q-values will be calculated instead of the FDRs</td>
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<td style="vertical-align:top"><b>use_all_hits</b></td>
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<td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
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<td style="vertical-align:top">true, false</td><td style="vertical-align:top">If 'true' not only the first hit, but all are used (peptides only)</td>
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<td style="vertical-align:top"><b>split_charge_variants</b></td>
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<td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
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<td style="vertical-align:top">true, false</td><td style="vertical-align:top">If set to 'true' charge variants are treated separately (for peptides of combined target/decoy searches only).</td>
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<td style="vertical-align:top"><b>treat_runs_separately</b></td>
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<td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
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<td style="vertical-align:top">true, false</td><td style="vertical-align:top">If set to 'true' different search runs are treated separately (for peptides of combined target/decoy searches only).</td>
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<td style="vertical-align:top"><b>decoy_string</b></td>
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<td style="vertical-align:top">string</td><td style="vertical-align:top">_rev</td>
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<td style="vertical-align:top"> </td><td style="vertical-align:top">String which is appended at the accession of the protein to indicate that it is a decoy protein (for proteins only).</td>
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<td style="vertical-align:top"><b>add_decoy_peptides</b></td>
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<td style="vertical-align:top">string</td><td style="vertical-align:top">false</td>
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<td style="vertical-align:top">true, false</td><td style="vertical-align:top">If set to true, decoy peptides will be written to output file, too. The q-value is set to the closest target score.</td>
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<UL style="margin-top:0px;">
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<LI> If a section name is documented, the documentation is displayed as tooltip.
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<LI> Advanced parameter names are italic.
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</div><h2 class="groupheader">Constructor & Destructor Documentation</h2>
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<td class="memname"><a class="el" href="classOpenMS_1_1FalseDiscoveryRate.html">FalseDiscoveryRate</a> </td>
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<td class="paramname"></td><td>)</td>
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<p>Default constructor. </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1FalseDiscoveryRate.html">FalseDiscoveryRate</a> </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1FalseDiscoveryRate.html">FalseDiscoveryRate</a> & </td>
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<td class="paramname"></td><td>)</td>
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<p>Not implemented. </p>
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<h2 class="groupheader">Member Function Documentation</h2>
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<td class="memname">void apply </td>
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<td class="paramtype">std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > & </td>
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<td class="paramname"><em>fwd_ids</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype">std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > & </td>
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<td class="paramname"><em>rev_ids</em> </td>
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<p>Calculates the FDR of two runs, a forward run and a decoy run on peptide level. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<table class="params">
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<tr><td class="paramname">fwd_ids</td><td>forward peptide identifications </td></tr>
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<tr><td class="paramname">rev_ids</td><td>reverse peptide identifications </td></tr>
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<p>Referenced by <a class="el" href="classOpenMS_1_1IDEvaluationBase.html#af3a6dd04dd533f5b5eead2736eefe91f">IDEvaluationBase::getPoints()</a>.</p>
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<td class="memname">void apply </td>
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<td class="paramtype">std::vector< <a class="el" href="classOpenMS_1_1PeptideIdentification.html">PeptideIdentification</a> > & </td>
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<td class="paramname"><em>id</em></td><td>)</td>
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<p>Calculates the FDR of one run from a concatenated sequence db search. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<tr><td class="paramname">id</td><td>peptide identifications, containing target and decoy hits </td></tr>
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<td class="memname">void apply </td>
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<td class="paramtype">std::vector< <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> > & </td>
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<td class="paramname"><em>fwd_ids</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype">std::vector< <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> > & </td>
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<td class="paramname"><em>rev_ids</em> </td>
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<p>Calculates the FDR of two runs, a forward run and decoy run on protein level. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<table class="params">
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<tr><td class="paramname">fwd_ids</td><td>forward protein identifications </td></tr>
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<tr><td class="paramname">rev_ids</td><td>reverse protein identifications </td></tr>
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<td class="memname">void apply </td>
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<td class="paramtype">std::vector< <a class="el" href="classOpenMS_1_1ProteinIdentification.html">ProteinIdentification</a> > & </td>
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<td class="paramname"><em>ids</em></td><td>)</td>
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<p>Calculate the FDR of one run from a concatenated sequence db search. </p>
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<dl class="params"><dt>Parameters</dt><dd>
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<table class="params">
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<tr><td class="paramname">ids</td><td>protein identifications, containing target and decoy hits </td></tr>
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<td class="memname">void calculateFDRs_ </td>
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<td class="paramtype"><a class="el" href="classOpenMS_1_1Map.html">Map</a>< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a>, <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > & </td>
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<td class="paramname"><em>score_to_fdr</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype">std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > & </td>
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<td class="paramname"><em>target_scores</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype">std::vector< <a class="el" href="group__Concept.html#gace75bfb1aba684e874dffee13738bd15">DoubleReal</a> > & </td>
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<td class="paramname"><em>decoy_scores</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype">bool </td>
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<td class="paramname"><em>q_value</em>, </td>
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<td class="paramkey"></td>
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<td class="paramtype">bool </td>
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<td class="paramname"><em>higher_score_better</em> </td>
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<p>calculates the fdr stored into fdrs, given two vectors of scores </p>
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<td class="memname"><a class="el" href="classOpenMS_1_1FalseDiscoveryRate.html">FalseDiscoveryRate</a>& operator= </td>
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<td class="paramtype">const <a class="el" href="classOpenMS_1_1FalseDiscoveryRate.html">FalseDiscoveryRate</a> & </td>
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<td class="paramname"></td><td>)</td>
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<p>Not implemented. </p>
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<TABLE width="100%" border="0">
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
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<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:26 using doxygen 1.8.5</font></TD>
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