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<a href="#scatter-distribution-plot-allele-frequency-comparison" class="md-skip">
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<input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">





<label class="md-nav__link md-nav__link--active" for="__toc">


<span class="md-ellipsis">
Allele Frequency Comparison
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</a>



<nav class="md-nav md-nav--secondary" aria-label="Table of contents">






<label class="md-nav__title" for="__toc">
<span class="md-nav__icon md-icon"></span>
Table of contents
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<li class="md-nav__item">
<a href="#check_af" class="md-nav__link">
<span class="md-ellipsis">
.check_af()
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<li class="md-nav__item">
<a href="#plot_daf" class="md-nav__link">
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.plot_daf()
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Examples
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<label class="md-nav__title" for="__toc">
<span class="md-nav__icon md-icon"></span>
Table of contents
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<ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>

<li class="md-nav__item">
<a href="#check_af" class="md-nav__link">
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.check_af()
</span>
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.plot_daf()
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Examples
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<h1>Allele Frequency Comparison</h1>

<p>Scatter &amp; Distribution plot : allele frequency comparison</p>
<p>Available from v3.4.15</p>
<h1 id="scatter-distribution-plot-allele-frequency-comparison">Scatter &amp; Distribution plot : allele frequency comparison</h1>
<p>!! info "Available from v3.4.15"</p>
<h2 id="check_af">.check_af()</h2>
<div class="language-text highlight"><pre><span></span><code><span id="__span-0-1"><a id="__codelineno-0-1" name="__codelineno-0-1" href="#__codelineno-0-1"></a>#check the difference between the EAF in the sumstats and the allele frequency in VCF files
</span><span id="__span-0-2"><a id="__codelineno-0-2" name="__codelineno-0-2" href="#__codelineno-0-2"></a>sumstats.check_af()
</span><span id="__span-0-3"><a id="__codelineno-0-3" name="__codelineno-0-3" href="#__codelineno-0-3"></a>
</span><span id="__span-0-4"><a id="__codelineno-0-4" name="__codelineno-0-4" href="#__codelineno-0-4"></a>#allele frequnecy correlation plot
</span><span id="__span-0-5"><a id="__codelineno-0-5" name="__codelineno-0-5" href="#__codelineno-0-5"></a>sumstats.plot_daf()
</span></code></pre></div>
<h2 id="plot_daf">.plot_daf()</h2>
<div class="language-text highlight"><pre><span></span><code><span id="__span-1-1"><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>#allele frequnecy correlation plot
</span><span id="__span-1-2"><a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a>sumstats.plot_daf()
</span></code></pre></div>
<p>You need to run 'check_af()' first before plotting. For check_af(), see <a href="https://cloufield.github.io/gwaslab/Harmonization/#check-the-difference-in-allele-frequency">here</a>.</p>
<p>Options for <code>plot_daf</code>:
<code>threshold</code>: <code>float</code>, the threshold used to determine outliers.</p>
<h2 id="examples">Examples</h2>
<div class="admonition example">
<p class="admonition-title">Example</p>
<p><div class="language-text highlight"><pre><span></span><code><span id="__span-1-1"><a id="__codelineno-1-1" name="__codelineno-1-1" href="#__codelineno-1-1"></a>mysumstats = gl.Sumstats(&quot;t2d_bbj.txt.gz&quot;,
</span><span id="__span-1-2"><a id="__codelineno-1-2" name="__codelineno-1-2" href="#__codelineno-1-2"></a> snpid=&quot;SNP&quot;,
</span><span id="__span-1-3"><a id="__codelineno-1-3" name="__codelineno-1-3" href="#__codelineno-1-3"></a> chrom=&quot;CHR&quot;,
</span><span id="__span-1-4"><a id="__codelineno-1-4" name="__codelineno-1-4" href="#__codelineno-1-4"></a> pos=&quot;POS&quot;,
</span><span id="__span-1-5"><a id="__codelineno-1-5" name="__codelineno-1-5" href="#__codelineno-1-5"></a> ea=&quot;ALT&quot;,
</span><span id="__span-1-6"><a id="__codelineno-1-6" name="__codelineno-1-6" href="#__codelineno-1-6"></a> nea=&quot;REF&quot;,
</span><span id="__span-1-7"><a id="__codelineno-1-7" name="__codelineno-1-7" href="#__codelineno-1-7"></a> neaf=&quot;Frq&quot;,
</span><span id="__span-1-8"><a id="__codelineno-1-8" name="__codelineno-1-8" href="#__codelineno-1-8"></a> beta=&quot;BETA&quot;,
</span><span id="__span-1-9"><a id="__codelineno-1-9" name="__codelineno-1-9" href="#__codelineno-1-9"></a> se=&quot;SE&quot;,
</span><span id="__span-1-10"><a id="__codelineno-1-10" name="__codelineno-1-10" href="#__codelineno-1-10"></a> p=&quot;P&quot;,
</span><span id="__span-1-11"><a id="__codelineno-1-11" name="__codelineno-1-11" href="#__codelineno-1-11"></a> direction=&quot;Dir&quot;,
</span><span id="__span-1-12"><a id="__codelineno-1-12" name="__codelineno-1-12" href="#__codelineno-1-12"></a> n=&quot;N&quot;,nrows=10000)
</span><span id="__span-1-13"><a id="__codelineno-1-13" name="__codelineno-1-13" href="#__codelineno-1-13"></a>
</span><span id="__span-1-14"><a id="__codelineno-1-14" name="__codelineno-1-14" href="#__codelineno-1-14"></a># harmonize
</span><span id="__span-1-15"><a id="__codelineno-1-15" name="__codelineno-1-15" href="#__codelineno-1-15"></a>mysumstats.harmonize(basic_check = True,
</span><span id="__span-1-16"><a id="__codelineno-1-16" name="__codelineno-1-16" href="#__codelineno-1-16"></a> ref_seq=gl.get_path(&quot;ucsc_genome_hg19&quot;))
<p><div class="language-text highlight"><pre><span></span><code><span id="__span-2-1"><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a>mysumstats = gl.Sumstats(&quot;t2d_bbj.txt.gz&quot;,
</span><span id="__span-2-2"><a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a> snpid=&quot;SNP&quot;,
</span><span id="__span-2-3"><a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a> chrom=&quot;CHR&quot;,
</span><span id="__span-2-4"><a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a> pos=&quot;POS&quot;,
</span><span id="__span-2-5"><a id="__codelineno-2-5" name="__codelineno-2-5" href="#__codelineno-2-5"></a> ea=&quot;ALT&quot;,
</span><span id="__span-2-6"><a id="__codelineno-2-6" name="__codelineno-2-6" href="#__codelineno-2-6"></a> nea=&quot;REF&quot;,
</span><span id="__span-2-7"><a id="__codelineno-2-7" name="__codelineno-2-7" href="#__codelineno-2-7"></a> neaf=&quot;Frq&quot;,
</span><span id="__span-2-8"><a id="__codelineno-2-8" name="__codelineno-2-8" href="#__codelineno-2-8"></a> beta=&quot;BETA&quot;,
</span><span id="__span-2-9"><a id="__codelineno-2-9" name="__codelineno-2-9" href="#__codelineno-2-9"></a> se=&quot;SE&quot;,
</span><span id="__span-2-10"><a id="__codelineno-2-10" name="__codelineno-2-10" href="#__codelineno-2-10"></a> p=&quot;P&quot;,
</span><span id="__span-2-11"><a id="__codelineno-2-11" name="__codelineno-2-11" href="#__codelineno-2-11"></a> direction=&quot;Dir&quot;,
</span><span id="__span-2-12"><a id="__codelineno-2-12" name="__codelineno-2-12" href="#__codelineno-2-12"></a> n=&quot;N&quot;,nrows=10000)
</span><span id="__span-2-13"><a id="__codelineno-2-13" name="__codelineno-2-13" href="#__codelineno-2-13"></a>
</span><span id="__span-2-14"><a id="__codelineno-2-14" name="__codelineno-2-14" href="#__codelineno-2-14"></a># harmonize
</span><span id="__span-2-15"><a id="__codelineno-2-15" name="__codelineno-2-15" href="#__codelineno-2-15"></a>mysumstats.harmonize(basic_check = True,
</span><span id="__span-2-16"><a id="__codelineno-2-16" name="__codelineno-2-16" href="#__codelineno-2-16"></a> ref_seq=gl.get_path(&quot;ucsc_genome_hg19&quot;))
</span></code></pre></div>
<img width=600 src="https://github.com/Cloufield/gwaslab/assets/40289485/dc3716d6-1b85-42dd-99ca-d0a38a3ad6a1"></p>
<p><div class="language-text highlight"><pre><span></span><code><span id="__span-2-1"><a id="__codelineno-2-1" name="__codelineno-2-1" href="#__codelineno-2-1"></a># check the difference in allele frequency with reference vcf
</span><span id="__span-2-2"><a id="__codelineno-2-2" name="__codelineno-2-2" href="#__codelineno-2-2"></a>mysumstats.check_af(ref_infer=gl.get_path(&quot;1kg_eas_hg19&quot;),
</span><span id="__span-2-3"><a id="__codelineno-2-3" name="__codelineno-2-3" href="#__codelineno-2-3"></a> ref_alt_freq=&quot;AF&quot;,
</span><span id="__span-2-4"><a id="__codelineno-2-4" name="__codelineno-2-4" href="#__codelineno-2-4"></a> n_cores=2)
<p><div class="language-text highlight"><pre><span></span><code><span id="__span-3-1"><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a># check the difference in allele frequency with reference vcf
</span><span id="__span-3-2"><a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>mysumstats.check_af(ref_infer=gl.get_path(&quot;1kg_eas_hg19&quot;),
</span><span id="__span-3-3"><a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a> ref_alt_freq=&quot;AF&quot;,
</span><span id="__span-3-4"><a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a> n_cores=2)
</span></code></pre></div>
<img width=600 src="https://github.com/Cloufield/gwaslab/assets/40289485/8cdc53b4-f661-40d6-a61b-ab5f23af6a4c"></p>
<p><div class="language-text highlight"><pre><span></span><code><span id="__span-3-1"><a id="__codelineno-3-1" name="__codelineno-3-1" href="#__codelineno-3-1"></a>plot and get the outliers
</span><span id="__span-3-2"><a id="__codelineno-3-2" name="__codelineno-3-2" href="#__codelineno-3-2"></a>outliers = mysumstats.plot_daf(threshold=0.12,
</span><span id="__span-3-3"><a id="__codelineno-3-3" name="__codelineno-3-3" href="#__codelineno-3-3"></a> save=&quot;af_correlation.png&quot;,
</span><span id="__span-3-4"><a id="__codelineno-3-4" name="__codelineno-3-4" href="#__codelineno-3-4"></a> save_args={&quot;dpi&quot;:300})
<p><div class="language-text highlight"><pre><span></span><code><span id="__span-4-1"><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>plot and get the outliers
</span><span id="__span-4-2"><a id="__codelineno-4-2" name="__codelineno-4-2" href="#__codelineno-4-2"></a>outliers = mysumstats.plot_daf(threshold=0.12,
</span><span id="__span-4-3"><a id="__codelineno-4-3" name="__codelineno-4-3" href="#__codelineno-4-3"></a> save=&quot;af_correlation.png&quot;,
</span><span id="__span-4-4"><a id="__codelineno-4-4" name="__codelineno-4-4" href="#__codelineno-4-4"></a> save_args={&quot;dpi&quot;:300})
</span></code></pre></div>
<img width=600 src="https://github.com/Cloufield/gwaslab/assets/40289485/0e9c92d4-3bea-4734-8ba6-76f7fc6e329b"></p>
<p><div class="language-text highlight"><pre><span></span><code><span id="__span-4-1"><a id="__codelineno-4-1" name="__codelineno-4-1" href="#__codelineno-4-1"></a>outliers[1]
<p><div class="language-text highlight"><pre><span></span><code><span id="__span-5-1"><a id="__codelineno-5-1" name="__codelineno-5-1" href="#__codelineno-5-1"></a>outliers[1]
</span></code></pre></div>
<img width=600 src="https://github.com/Cloufield/gwaslab/assets/40289485/c99d91cb-f1f8-4412-bfbf-960457fc9d0e"></p>
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