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detectBatchDiff.html
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<title>Detect batch/block differences — detectBatchDiff • metaboMisc</title>
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<h1>Detect batch/block differences</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>detectBatchDiff.Rd</code></div>
</div>
<div class="ref-description">
<p>Detect batch/block differences within analytical runs for each ionisation mode.</p>
</div>
<pre class="usage"><span class='fu'>detectBatchDiff</span><span class='op'>(</span><span class='va'>x</span>, by <span class='op'>=</span> <span class='st'>"block"</span>, pthresh <span class='op'>=</span> <span class='fl'>0.05</span><span class='op'>)</span>
<span class='co'># S4 method for Binalysis</span>
<span class='fu'>detectBatchDiff</span><span class='op'>(</span><span class='va'>x</span>, by <span class='op'>=</span> <span class='st'>"block"</span>, pthresh <span class='op'>=</span> <span class='fl'>0.05</span><span class='op'>)</span>
<span class='co'># S4 method for MetaboProfile</span>
<span class='fu'>detectBatchDiff</span><span class='op'>(</span><span class='va'>x</span>, by <span class='op'>=</span> <span class='st'>"block"</span>, pthresh <span class='op'>=</span> <span class='fl'>0.05</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>object of class <code>Binalysis</code> or <code>MetaboProfile</code></p></td>
</tr>
<tr>
<th>by</th>
<td><p>info class column to use for batch information</p></td>
</tr>
<tr>
<th>pthresh</th>
<td><p>p-value threshold for significance</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>If no differences between batches are found then <code>NULL</code> is returned. If significant differences are found then a tibble is returned containing the ANOVA results for each ionisation mode and showing whether batch correction is needed.</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Analysis of Variance (ANOVA) is used to detect differences in total ion count (TIC) averages between batches/blocks.</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'><-</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'><-</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'><-</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'>#> <span class='message'></span>
#> <span class='message'>Attaching package: ‘purrr’</span></div><div class='output co'>#> <span class='message'>The following object is masked from ‘package:metaboMisc’:</span>
#> <span class='message'></span>
#> <span class='message'> reduce</span></div><div class='output co'>#> <span class='message'><span style='color: #0000BB;'>binneR</span> <span style='color: #BB0000;'>v2.5.3</span> Mon Sep 27 11:19:18 2021</span></div><div class='output co'>#> <span class='message'>________________________________________________________________________________</span></div><div class='output co'>#> <span class='message'>Scans: 5:14 </span></div><div class='output co'>#> <span class='message'>________________________________________________________________________________</span></div><div class='output co'>#> <span class='message'>Reading raw data</span></div><div class='output co'>#> <span class='message'>Gathering bins</span></div><div class='output co'>#> <span class='message'>Removing single scan events</span></div><div class='output co'>#> <span class='message'>Averaging intensities across scans</span></div><div class='output co'>#> <span class='message'>Calculating bin metrics</span></div><div class='output co'>#> <span class='message'>Calculating accurate m/z</span></div><div class='output co'>#> <span class='message'>Building intensity matrix</span></div><div class='output co'>#> <span class='message'>Gathering file headers</span></div><div class='output co'>#> </div><div class='output co'>#> <span class='message'><span style='color: #00BB00;'>Completed! </span>[2.9S]</span></div><div class='input'>
<span class='co'>## Detect batch differences</span>
<span class='va'>batch_diff</span> <span class='op'><-</span> <span class='fu'>detectBatchDiff</span><span class='op'>(</span><span class='va'>analysis</span><span class='op'>)</span>
</div><div class='output co'>#> <span class='message'>Batches with < 3 replicates removed: "3", "5"</span></div><div class='output co'>#> <span class='message'>Only 1 batch detected, skipping detection</span></div><div class='input'>
<span class='co'>## Display batch diffferences</span>
<span class='va'>batch_diff</span>
</div><div class='output co'>#> NULL</div></pre>
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