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<div class="title">FFEval </div>  </div>
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<div class="textblock"><p>Evaluation tool for feature detection algorithms.</p>
<p>To plot the ROC curve you might use:</p>
<div class="fragment"><div class="line">d = read.table(<span class="stringliteral">&quot;data.roc&quot;</span>, skip=1, sep=<span class="stringliteral">&quot;\t&quot;</span>)</div>
<div class="line">plot(d[,3],d[,4], xlim=<a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>(0,1),ylim=<a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>(0,1), xlab=<span class="stringliteral">&quot;FDR&quot;</span>,ylab=<span class="stringliteral">&quot;TPR&quot;</span>,<a class="code" href="RNPxl_8C.html#a217dbf8b442f20279ea00b898af96f52">main</a>=<span class="stringliteral">&quot;ROC with varying intensity&quot;</span>)</div>
<div class="line">lines(<a class="code" href="namespaceOpenMS_1_1Constants.html#a8fc6defe4e499b1b9b9c275689e44352">c</a>(0,1),c(0,1))</div>
</div><!-- fragment --><p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
FFEval -- Evaluation tool for feature detection algorithms.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976

Usage:
  FFEval &lt;options&gt;

Options (mandatory options marked with '*'):
  -in &lt;file&gt;*            Feature input file, which contains the data to be tested against the truth file. 
                         (valid formats: 'featureXML')
  -truth &lt;file&gt;*         Truth feature file that defines what features should be found. (valid formats: 'feat
                         ureXML')
  -rt_tol &lt;double&gt;       Allowed tolerance of RT relative to average feature RT span. (default: '0.3' min: 
                         '0')
  -rt_tol_abs &lt;double&gt;   Allowed absolute tolerance of RT (overwrites 'rt_tol' if set above zero). (default: 
                         '-1' min: '-1')
  -mz_tol &lt;double&gt;       Allowed tolerance in m/z (is divided by charge). (default: '0.25' min: '0')
  -out &lt;file&gt;            Feature output file. If given, an annotated input file is written. (valid formats: 
                         'featureXML')
  -abort_reasons &lt;file&gt;  Feature file containing seeds with abort reasons. (valid formats: 'featureXML')
  -out_roc &lt;file&gt;        If given, a ROC curve file is created (ROC points based on intensity threshold) (val
                         id formats: 'csv')
                         
Common UTIL options:
  -ini &lt;file&gt;            Use the given TOPP INI file
  -threads &lt;n&gt;           Sets the number of threads allowed to be used by the TOPP tool (default: '1')
  -write_ini &lt;file&gt;      Writes the default configuration file
  --help                 Shows options
  --helphelp             Shows all options (including advanced)

</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">+FFEval</span><span class="node_description">Evaluation tool for feature detection algorithms.</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 'FFEval'</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">Feature input file, which contains the data to be tested against the truth file.</span><span class="item_tags">input file</span><span class="item_restrictions">*.featureXML</span></div>      <div class="item"><span class="item_name item_required" style="padding-left:24px;">truth</span><span class="item_value"></span>
<span class="item_description">Truth feature file that defines what features should be found.</span><span class="item_tags">input file</span><span class="item_restrictions">*.featureXML</span></div>      <div class="item"><span class="item_name" style="padding-left:24px;">rt_tol</span><span class="item_value">0.3</span>
<span class="item_description">Allowed tolerance of RT relative to average feature RT span.</span><span class="item_tags"></span><span class="item_restrictions">0:&#8734;</span></div>      <div class="item"><span class="item_name" style="padding-left:24px;">rt_tol_abs</span><span class="item_value">-1</span>
<span class="item_description">Allowed absolute tolerance of RT (overwrites 'rt_tol' if set above zero).</span><span class="item_tags"></span><span class="item_restrictions">-1:&#8734;</span></div>      <div class="item"><span class="item_name" style="padding-left:24px;">mz_tol</span><span class="item_value">0.25</span>
<span class="item_description">Allowed tolerance in m/z (is divided by charge).</span><span class="item_tags"></span><span class="item_restrictions">0:&#8734;</span></div>      <div class="item"><span class="item_name" style="padding-left:24px;">out</span><span class="item_value"></span>
<span class="item_description">Feature output file. If given, an annotated input file is written.</span><span class="item_tags">output file</span><span class="item_restrictions">*.featureXML</span></div>      <div class="item"><span class="item_name" style="padding-left:24px;">abort_reasons</span><span class="item_value"></span>
<span class="item_description">Feature file containing seeds with abort reasons.</span><span class="item_tags">input file</span><span class="item_restrictions">*.featureXML</span></div>      <div class="item"><span class="item_name" style="padding-left:24px;">out_roc</span><span class="item_value"></span>
<span class="item_description">If given, a ROC curve file is created (ROC points based on intensity threshold)</span><span class="item_tags">output file</span><span class="item_restrictions">*.csv</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>
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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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