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    <h1>Detect modelling parameters</h1>
    <small class="dont-index">Source: <a href='https://github.com/jasenfinch/metaboMisc/blob/master/R/detect.R'><code>R/detect.R</code></a></small>
    <div class="hidden name"><code>detectModellingParameters.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>Detect modelling parameters for <code>Binalysis</code>, <code>MetaboProfile</code> or <code>Analysis</code> S4 classes.</p>
    </div>

    <pre class="usage"><span class='fu'>detectModellingParameters</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span>

<span class='co'># S4 method for Binalysis</span>
<span class='fu'>detectModellingParameters</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>

<span class='co'># S4 method for MetaboProfile</span>
<span class='fu'>detectModellingParameters</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>

<span class='co'># S4 method for Analysis</span>
<span class='fu'>detectModellingParameters</span><span class='op'>(</span><span class='va'>x</span>, type <span class='op'>=</span> <span class='st'>"pre-treated"</span>, cls <span class='op'>=</span> <span class='st'>"class"</span><span class='op'>)</span></pre>

    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
    <table class="ref-arguments">
    <colgroup><col class="name" /><col class="desc" /></colgroup>
    <tr>
      <th>x</th>
      <td><p>S4 object of class <code>Binalysis</code>,<code>MetaboProfile</code> or <code>Analysis</code></p></td>
    </tr>
    <tr>
      <th>...</th>
      <td><p>arguments to pass to the appropriate method</p></td>
    </tr>
    <tr>
      <th>type</th>
      <td><p>detect parameters for <code>raw</code> or <code>pre-treated</code> data for <code>Analysis</code> class</p></td>
    </tr>
    <tr>
      <th>cls</th>
      <td><p>sample information column to use for modelling</p></td>
    </tr>
    </table>

    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>

    <p>S4 object of class <code>AnalysisParameters</code></p>

    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
    <pre class="examples"><div class='input'><span class='co'>## Retrieve file paths and sample information for example data</span>
<span class='va'>files</span> <span class='op'>&lt;-</span> <span class='fu'>metaboData</span><span class='fu'>::</span><span class='fu'><a href='https://aberHRML.github.io/metaboData//reference/filePaths.html'>filePaths</a></span><span class='op'>(</span><span class='st'>'FIE-HRMS'</span>,<span class='st'>'BdistachyonEcotypes'</span><span class='op'>)</span><span class='op'>[</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>2</span><span class='op'>]</span>

<span class='va'>info</span> <span class='op'>&lt;-</span> <span class='fu'>metaboData</span><span class='fu'>::</span><span class='fu'><a href='https://aberHRML.github.io/metaboData//reference/runinfo.html'>runinfo</a></span><span class='op'>(</span><span class='st'>'FIE-HRMS'</span>,<span class='st'>'BdistachyonEcotypes'</span><span class='op'>)</span><span class='op'>[</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>2</span>,<span class='op'>]</span>

<span class='co'>## Perform spectral binning</span>
<span class='va'>analysis</span> <span class='op'>&lt;-</span> <span class='fu'>binneR</span><span class='fu'>::</span><span class='fu'><a href='https://aberHRML.github.io/binneR/reference/binneRlyse.html'>binneRlyse</a></span><span class='op'>(</span><span class='va'>files</span>, 
                               <span class='va'>info</span>, 
                               parameters <span class='op'>=</span> <span class='fu'>binneR</span><span class='fu'>::</span><span class='fu'><a href='https://aberHRML.github.io/binneR/reference/detectParameters.html'>detectParameters</a></span><span class='op'>(</span><span class='va'>files</span><span class='op'>)</span><span class='op'>)</span>
</div><div class='output co'>#&gt; <span class='message'><span style='color: #0000BB;'>binneR</span> <span style='color: #BB0000;'>v2.5.3</span> Mon Sep 27 11:19:25 2021</span></div><div class='output co'>#&gt; <span class='message'>________________________________________________________________________________</span></div><div class='output co'>#&gt; <span class='message'>Scans: 5:14 </span></div><div class='output co'>#&gt; <span class='message'>________________________________________________________________________________</span></div><div class='output co'>#&gt; <span class='message'>Reading raw data</span></div><div class='output co'>#&gt; <span class='message'>Gathering bins</span></div><div class='output co'>#&gt; <span class='message'>Removing single scan events</span></div><div class='output co'>#&gt; <span class='message'>Averaging intensities across scans</span></div><div class='output co'>#&gt; <span class='message'>Calculating bin metrics</span></div><div class='output co'>#&gt; <span class='message'>Calculating accurate m/z</span></div><div class='output co'>#&gt; <span class='message'>Building intensity matrix</span></div><div class='output co'>#&gt; <span class='message'>Gathering file headers</span></div><div class='output co'>#&gt; </div><div class='output co'>#&gt; <span class='message'><span style='color: #00BB00;'>Completed! </span>[2.2S]</span></div><div class='input'>
<span class='co'>## Detect modelling parameters</span>
<span class='va'>modelling_parameters</span> <span class='op'>&lt;-</span> <span class='fu'>detectModellingParameters</span><span class='op'>(</span><span class='va'>analysis</span><span class='op'>)</span>

<span class='va'>modelling_parameters</span>
</div><div class='output co'>#&gt; <span style='color: #BBBB00;'>Parameters:</span>
#&gt; </div></pre>
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