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<title>Generic harmonisation function — harmonise • gwasglue</title>
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<h1>Generic harmonisation function</h1>
<small class="dont-index">Source: <a href='https://github.com/mrcieu/gwasglue/blob/master/R/harmonise.r'><code>R/harmonise.r</code></a></small>
<div class="hidden name"><code>harmonise.Rd</code></div>
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<div class="ref-description">
<p>Assumes ref and alt alleles available for target and reference datasets, and uses chr:pos for alignment</p>
</div>
<pre class="usage"><span class='fu'>harmonise</span><span class='op'>(</span>
<span class='va'>chr1</span>,
<span class='va'>pos1</span>,
<span class='va'>ref1</span>,
<span class='va'>alt1</span>,
<span class='va'>chr2</span>,
<span class='va'>pos2</span>,
<span class='va'>ref2</span>,
<span class='va'>alt2</span>,
rsid2 <span class='op'>=</span> <span class='cn'>NULL</span>,
indel_recode <span class='op'>=</span> <span class='cn'>FALSE</span>,
strand_flip <span class='op'>=</span> <span class='cn'>FALSE</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>chr1</th>
<td><p>Vector</p></td>
</tr>
<tr>
<th>pos1</th>
<td><p>Vector</p></td>
</tr>
<tr>
<th>ref1</th>
<td><p>Vector</p></td>
</tr>
<tr>
<th>alt1</th>
<td><p>Vector</p></td>
</tr>
<tr>
<th>chr2</th>
<td><p>Vector</p></td>
</tr>
<tr>
<th>pos2</th>
<td><p>Vector</p></td>
</tr>
<tr>
<th>ref2</th>
<td><p>Vector</p></td>
</tr>
<tr>
<th>alt2</th>
<td><p>Vector</p></td>
</tr>
<tr>
<th>rsid2</th>
<td><p>Optional vector</p></td>
</tr>
<tr>
<th>indel_recode</th>
<td><p>=FALSE. If TRUE then attempts to recode D/I</p></td>
</tr>
<tr>
<th>strand_flip</th>
<td><p>=FALSE. If TRUE then attempts to flip strand when alignment is not otherwise possible</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Dataframe of outcomes</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>0: stick
1: swap
2: rename indel
3: rename indel and swap
4: flip
5: flip and swap
6: drop (no match)
7: drop (no reference)</p>
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