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iso_remove_problematic_peak_mappings.html
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iso_remove_problematic_peak_mappings.html
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<h1>Remove problematic peak mappings</h1>
<small class="dont-index">Source: <a href='https://github.com/isoverse/isoprocessor/blob/master/R/peak_mapping.R'><code>R/peak_mapping.R</code></a></small>
<div class="hidden name"><code>iso_remove_problematic_peak_mappings.Rd</code></div>
</div>
<div class="ref-description">
<p>Remove peak mappings that were problematic (unidentified, missing, or ambiguous) during peak mapping.</p>
</div>
<pre class="usage"><span class='fu'>iso_remove_problematic_peak_mappings</span><span class='op'>(</span><span class='va'>...</span><span class='op'>)</span>
<span class='co'># S3 method for iso_file_list</span>
<span class='fu'>iso_remove_problematic_peak_mappings</span><span class='op'>(</span>
<span class='va'>iso_files</span>,
remove_unidentified <span class='op'>=</span> <span class='cn'>TRUE</span>,
remove_missing <span class='op'>=</span> <span class='cn'>TRUE</span>,
remove_ambiguous <span class='op'>=</span> <span class='cn'>TRUE</span>,
remove_mapping_info_columns <span class='op'>=</span> <span class='cn'>TRUE</span>,
quiet <span class='op'>=</span> <span class='fu'>default</span><span class='op'>(</span><span class='va'>quiet</span><span class='op'>)</span>
<span class='op'>)</span>
<span class='co'># S3 method for data.frame</span>
<span class='fu'>iso_remove_problematic_peak_mappings</span><span class='op'>(</span>
<span class='va'>peak_table</span>,
remove_unidentified <span class='op'>=</span> <span class='cn'>TRUE</span>,
remove_missing <span class='op'>=</span> <span class='cn'>TRUE</span>,
remove_ambiguous <span class='op'>=</span> <span class='cn'>TRUE</span>,
remove_mapping_info_columns <span class='op'>=</span> <span class='cn'>TRUE</span>,
quiet <span class='op'>=</span> <span class='fu'>default</span><span class='op'>(</span><span class='va'>quiet</span><span class='op'>)</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>...</th>
<td><p>S3 method placeholder parameters, see class specific functions for details on parameters</p></td>
</tr>
<tr>
<th>iso_files</th>
<td><p>collection of continuous flow iso_file objects</p></td>
</tr>
<tr>
<th>quiet</th>
<td><p>whether to display (quiet=FALSE) or silence (quiet = TRUE) information messages. Set parameter to overwrite global defaults for this function or set global defaults with calls to <a href='https://rdrr.io/pkg/isoreader/man/iso_info_messages.html'>iso_turn_info_message_on</a> and <a href='https://rdrr.io/pkg/isoreader/man/iso_info_messages.html'>iso_turn_info_message_off</a></p></td>
</tr>
<tr>
<th>peak_table</th>
<td><p>data frame with mapped peaks. Requires the <code>is_identified</code>, <code>is_missing</code> and <code>is_ambiguous</code> columns to be present.</p></td>
</tr>
<tr>
<th>remove_mapping_info_column</th>
<td><p>whether to automatically remove mapping info columns. If true and:</p><ul>
<li><p><code>remove_unidentified = TRUE</code> - <code>is_identified</code> column automatically removed</p></li>
<li><p><code>remove_missing = TRUE</code> - <code>is_missing</code> column automatically removed</p></li>
<li><p><code>remove_ambiguous = TRUE</code> - <code>is_ambiguous</code>, <code>n_matches</code>, and <code>n_overlapping</code> columns automatically removed</p></li>
</ul></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>the data with the problematic peak mappings remove</p>
<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
<div class='dont-index'><p>Other peak mapping functions:
<code><a href='iso_get_problematic_peaks.html'>iso_get_problematic_peaks</a>()</code>,
<code><a href='iso_map_peaks.html'>iso_map_peaks</a>()</code>,
<code><a href='iso_summarize_peak_mappings.html'>iso_summarize_peak_mappings</a>()</code></p></div>
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