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<a href="../articles/cojo.html">Conditional analysis of VCF files</a>
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<h1>Reference</h1>
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<h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
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<p><code><a href="clump_gwasvcf.html">clump_gwasvcf()</a></code> </p>
</td>
<td><p>Perform LD clumping</p></td>
</tr><tr>
<td>
<p><code><a href="cojo_cond.html">cojo_cond()</a></code> </p>
</td>
<td><p>Perform conditional analysis using GCTA COJO</p></td>
</tr><tr>
<td>
<p><code><a href="cojo_sumstat_file.html">cojo_sumstat_file()</a></code> </p>
</td>
<td><p>Write vcf file to cojo sumstat file</p></td>
</tr><tr>
<td>
<p><code><a href="coloc_to_gassocplot.html">coloc_to_gassocplot()</a></code> </p>
</td>
<td><p>Convert coloc dataset to gassocplot dataset</p></td>
</tr><tr>
<td>
<p><code><a href="gwasvcf_to_TwoSampleMR.html">gwasvcf_to_TwoSampleMR()</a></code> </p>
</td>
<td><p>Create exposure or outcome data format for TwoSampleMR from vcf</p></td>
</tr><tr>
<td>
<p><code><a href="gwasvcf_to_coloc.html">gwasvcf_to_coloc()</a></code> </p>
</td>
<td><p>Generate coloc dataset from vcf files</p></td>
</tr><tr>
<td>
<p><code><a href="gwasvcf_to_finemapr.html">gwasvcf_to_finemapr()</a></code> </p>
</td>
<td><p>Generate data for fine mapping analysis</p></td>
</tr><tr>
<td>
<p><code><a href="harmonise.html">harmonise()</a></code> </p>
</td>
<td><p>Generic harmonisation function</p></td>
</tr><tr>
<td>
<p><code><a href="harmonise_against_ref.html">harmonise_against_ref()</a></code> </p>
</td>
<td><p>Harmonise gwas alleles to be same as reference</p></td>
</tr><tr>
<td>
<p><code><a href="ieugwasr_to_TwoSampleMR.html">ieugwasr_to_TwoSampleMR()</a></code> </p>
</td>
<td><p>Convert output from query to TwoSampleMR format</p></td>
</tr><tr>
<td>
<p><code><a href="ieugwasr_to_coloc.html">ieugwasr_to_coloc()</a></code> </p>
</td>
<td><p>Generate coloc dataset from the IEU GWAS database</p></td>
</tr><tr>
<td>
<p><code><a href="ieugwasr_to_finemapr.html">ieugwasr_to_finemapr()</a></code> </p>
</td>
<td><p>Generate data for analysis in various finemapping methods</p></td>
</tr><tr>
<td>
<p><code><a href="ieugwasr_to_gassocplot.html">ieugwasr_to_gassocplot()</a></code> </p>
</td>
<td><p>Generate regional plot for ieugwasr</p></td>
</tr><tr>
<td>
<p><code><a href="is_forward_strand.html">is_forward_strand()</a></code> </p>
</td>
<td><p>Check a GWAS dataset against a reference known to be on the forward strand</p></td>
</tr><tr>
<td>
<p><code><a href="make_TwoSampleMR_dat.html">make_TwoSampleMR_dat()</a></code> </p>
</td>
<td><p>Create a harmonised dataset from lists of vcf files</p></td>
</tr><tr>
<td>
<p><code><a href="map_variants_to_regions.html">map_variants_to_regions()</a></code> </p>
</td>
<td><p>For a set of variants map to LD regions</p></td>
</tr><tr>
<td>
<p><code><a href="organise_ids.html">organise_ids()</a></code> </p>
</td>
<td><p>Figure out specific files and IDs depending on what files exist and whethet vcfdir is set</p></td>
</tr><tr>
<td>
<p><code><a href="read_gwas.html">read_gwas()</a></code> </p>
</td>
<td><p>Read in GWAS dataset</p></td>
</tr><tr>
<td>
<p><code><a href="read_reference.html">read_reference()</a></code> </p>
</td>
<td><p>Read in reference dataset</p></td>
</tr><tr>
<td>
<p><code><a href="set_bc4_files.html">set_bc4_files()</a></code> </p>
</td>
<td><p>Determine locations of useful reference datasets on bluecrystal4</p></td>
</tr><tr>
<td>
<p><code><a href="susieR_pipeline.html">susieR_pipeline()</a></code> </p>
</td>
<td><p>Perform fine mapping pipeline using susieR</p></td>
</tr><tr>
<td>
<p><code><a href="write_out.html">write_out()</a></code> </p>
</td>
<td><p>Create format for HPC pipeline</p></td>
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