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calculate_backgrounds.html
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calculate_backgrounds.html
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<title>Calculate background signals — calculate_backgrounds • isoprocessor</title>
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<h1>Calculate background signals</h1>
<small class="dont-index">Source: <a href='https://github.com/isoverse/isoprocessor/blob/master/R/peak_calculations.R'><code>R/peak_calculations.R</code></a></small>
<div class="hidden name"><code>calculate_backgrounds.Rd</code></div>
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<div class="ref-description">
<p>This function calculates peak backgrounds from a chromatographic trace with peak table data (see <code><a href='iso_combine_raw_data_with_peak_table.html'>iso_combine_raw_data_with_peak_table</a></code>).</p>
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<pre class="usage"><span class='fu'>calculate_backgrounds</span>(
<span class='no'>data</span>,
<span class='no'>method</span>,
<span class='kw'>signal_pattern</span> <span class='kw'>=</span> <span class='st'>"^[vi]\\d+"</span>,
<span class='kw'>bg_suffix</span> <span class='kw'>=</span> <span class='st'>"_bgrd"</span>,
<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'>default</span>(<span class='st'>"time"</span>),
<span class='kw'>peak</span> <span class='kw'>=</span> <span class='fu'>default</span>(<span class='st'>"peak"</span>),
<span class='kw'>bgrd</span> <span class='kw'>=</span> <span class='fu'>default</span>(<span class='st'>"bgrd"</span>),
<span class='kw'>file</span> <span class='kw'>=</span> <span class='fu'>default</span>(<span class='st'>"file"</span>),
<span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fu'>default</span>(<span class='st'>"quiet"</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>data</th>
<td><p>the data frame with chromatographic and peak information</p></td>
</tr>
<tr>
<th>method</th>
<td><p>what method to use to calculate backgrounds (backgrounds are ALWAYS based solely on time points marked as background)
run_const = constant background averaged across entire run
run_linear = linear background across run @FIXME NOT IMPELEMENTED YET
peak_const = constant background across single peak @FIXME NOT IMPELEMENTED YET
peak_linear = linear background across peak @FIXME NOT IMPELEMENTED YET</p></td>
</tr>
<tr>
<th>signal_pattern</th>
<td><p>pattern for signal columns (by default detects voltages starting with e.g. v45 and currents starting with e.g. i45)</p></td>
</tr>
<tr>
<th>bg_suffix</th>
<td><p>the suffix for the new background columns</p></td>
</tr>
<tr>
<th>time</th>
<td><p>column name of the time column to use to find peak centers</p></td>
</tr>
<tr>
<th>peak</th>
<td><p>column name of the peak id column that identifies different peaks</p></td>
</tr>
<tr>
<th>file</th>
<td><p>column name of the filename column</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>data frame with new signal columns with bg_suffix added, as well as a p.calc_bgrd_method</p>
<h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
<p>perhaps implement possibilty to pass with an actual function as method that takes the sub data frame as parameter?</p>
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<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#note">Note</a></li>
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