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UKB_participantQC.html
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<title>Participant QC</title>
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Participant QC
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<h1 class="title toc-ignore">Participant QC</h1>
<h4 class="author">Mike Francis</h4>
<h4 class="date">2022-10-09 22:11:47</h4>
</div>
<p>The purpose of this script is to generate a list of UK Biobank
participants which meet QC/filtering criteria:</p>
<ol style="list-style-type: decimal">
<li>Genetic ethnicity = Caucasian via Pan UKBB designation</li>
<li>Not an outlier for heterogeneity and missing genotype rate (poor
quality genotype)</li>
<li>No sex chromosome aneuploidy</li>
<li>Self-reported sex matches genetic sex</li>
<li>Do not have high degree of genetic kinship (ten or more third-degree
relatives identified)</li>
<li>Does not appear in “maximum_set_of_unrelated_individuals.pl”</li>
</ol>
<div id="load-packages-make-it-so-table-always-displays-nas"
class="section level3">
<h3>Load packages + make it so table always displays NA’s</h3>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">suppressMessages</span>(silent <span class="ot"><-</span> <span class="fu">lapply</span>(</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">c</span>(<span class="st">"plyr"</span>, <span class="st">"dplyr"</span>, <span class="st">"tidyverse"</span>, <span class="st">"data.table"</span>, <span class="st">"vroom"</span>, <span class="st">"knitr"</span>), </span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a> library, <span class="at">character.only=</span>T))</span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a>table <span class="ot">=</span> <span class="cf">function</span> (..., <span class="at">useNA =</span> <span class="st">'always'</span>) base<span class="sc">::</span><span class="fu">table</span>(..., <span class="at">useNA =</span> useNA)</span></code></pre></div>
</div>
<div id="load-uk-biobank-data" class="section level3">
<h3>Load UK Biobank data</h3>
<pre><code>## [1] 502527 5172</code></pre>
<p>This code chunk has been modified for display to hide the 5-digit
code that came with our data table</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a>bd<span class="ot">=</span><span class="fu">vroom</span>(<span class="st">"/Users/mike/Documents/R_files/UKBpheno/pheno/ukbXXXXX.tab"</span>, <span class="at">delim=</span><span class="st">"</span><span class="sc">\t</span><span class="st">"</span>, <span class="at">show_col_types =</span> <span class="cn">FALSE</span>)</span>
<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a><span class="fu">source</span>(<span class="st">"src/components/ukbXXXXX_factordata.R"</span>) <span class="co">#file provided by UKB "ukbxxxxx_loaddata.R" without the loading part, to label the responses in survey questions</span></span>
<span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a>bd<span class="ot">=</span><span class="fu">as_tibble</span>(bd)</span>
<span id="cb3-4"><a href="#cb3-4" aria-hidden="true" tabindex="-1"></a><span class="fu">dim</span>(bd)</span>
<span id="cb3-5"><a href="#cb3-5" aria-hidden="true" tabindex="-1"></a>withdrawn<span class="ot"><-</span><span class="fu">read.csv</span>(<span class="st">"src/components/w48818_20220222.csv"</span>, <span class="at">header =</span> <span class="cn">FALSE</span>)</span>
<span id="cb3-6"><a href="#cb3-6" aria-hidden="true" tabindex="-1"></a>bd<span class="ot">=</span>bd[<span class="sc">!</span>(bd<span class="sc">$</span>f.eid <span class="sc">%in%</span> withdrawn<span class="sc">$</span>V1), ]</span></code></pre></div>
</div>
<div
id="load-the-files-that-came-from-pan-ukbb-list-of-participants-and-bridge-key"
class="section level3">
<h3>Load the files that came from Pan UKBB, list of participants and
bridge (key)</h3>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a>pan<span class="ot"><-</span><span class="fu">read_tsv</span>(<span class="st">"src/components/PanUKBB/all_pops_non_eur_pruned_within_pop_pc_covs.tsv"</span>)</span></code></pre></div>
<pre><code>## Rows: 448216 Columns: 28
## ── Column specification ─────────────────────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr (1): pop
## dbl (26): s, PC1, PC2, PC3, PC4, PC5, PC6, PC7, PC8, PC9, PC10, PC11, PC12, ...
## lgl (1): related
##
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.</code></pre>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a>pan<span class="ot"><-</span><span class="fu">as_tibble</span>(pan)</span>
<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a>pan<span class="sc">$</span>s<span class="ot"><-</span><span class="fu">as.integer</span>(pan<span class="sc">$</span>s)</span>
<span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a><span class="fu">table</span>(pan<span class="sc">$</span>pop)<span class="sc">%>%</span><span class="fu">kbl</span>()</span></code></pre></div>
<table>
<thead>
<tr>
<th style="text-align:left;">
Var1
</th>
<th style="text-align:right;">
Freq
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:left;">
AFR
</td>
<td style="text-align:right;">
6805
</td>
</tr>
<tr>
<td style="text-align:left;">
AMR
</td>
<td style="text-align:right;">
996
</td>
</tr>
<tr>
<td style="text-align:left;">
CSA
</td>
<td style="text-align:right;">
9109
</td>
</tr>
<tr>
<td style="text-align:left;">
EAS
</td>
<td style="text-align:right;">
2783
</td>
</tr>
<tr>
<td style="text-align:left;">
EUR
</td>
<td style="text-align:right;">
426901
</td>
</tr>
<tr>
<td style="text-align:left;">
MID
</td>
<td style="text-align:right;">
1622
</td>
</tr>
<tr>
<td style="text-align:left;">
NA
</td>
<td style="text-align:right;">
0
</td>
</tr>
</tbody>
</table>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a>bridge<span class="ot"><-</span><span class="fu">read.table</span>(<span class="st">"src/components/PanUKBB/ukb48818bridge31063.txt"</span>)</span>
<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a>bridge<span class="ot"><-</span><span class="fu">as_tibble</span>(bridge)</span>
<span id="cb7-3"><a href="#cb7-3" aria-hidden="true" tabindex="-1"></a><span class="fu">colnames</span>(bridge)<span class="ot"><-</span><span class="fu">c</span>(<span class="st">"IID"</span>, <span class="st">"panID"</span>)</span>
<span id="cb7-4"><a href="#cb7-4" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb7-5"><a href="#cb7-5" aria-hidden="true" tabindex="-1"></a>pan2<span class="ot"><-</span>pan<span class="sc">%>%</span><span class="fu">select</span>(s, pop)<span class="sc">%>%</span></span>
<span id="cb7-6"><a href="#cb7-6" aria-hidden="true" tabindex="-1"></a> <span class="fu">left_join</span>(bridge, <span class="at">by=</span><span class="fu">c</span>(<span class="st">"s"</span><span class="ot">=</span><span class="st">"panID"</span>))</span></code></pre></div>
</div>
<div id="retrieve-relevant-qc-columns-from-ukb" class="section level3">
<h3>Retrieve relevant QC columns from UKB</h3>
<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a>bd_QC<span class="ot"><-</span> bd <span class="sc">%>%</span> <span class="fu">select</span>(f.eid, f.<span class="dv">31</span>.<span class="fl">0.0</span>, f.<span class="dv">22001</span>.<span class="fl">0.0</span>, f.<span class="dv">21000</span>.<span class="fl">0.0</span>, f.<span class="dv">22027</span>.<span class="fl">0.0</span>, f.<span class="dv">22019</span>.<span class="fl">0.0</span>, f.<span class="dv">22021</span>.<span class="fl">0.0</span>)</span>
<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb8-3"><a href="#cb8-3" aria-hidden="true" tabindex="-1"></a><span class="fu">colnames</span>(bd_QC)<span class="ot"><-</span><span class="fu">c</span>(<span class="st">"IID"</span>, <span class="st">"Sex"</span>, <span class="st">"Genetic_Sex"</span>, <span class="st">"Race"</span>, <span class="st">"Outliers_for_het_or_missing"</span>, <span class="st">"SexchrAneuploidy"</span>, <span class="st">"Genetic_kinship"</span>)</span></code></pre></div>
</div>
<div id="join-ukb-cols-with-with-pan-ukbb" class="section level3">
<h3>Join UKB cols with with Pan UKBB</h3>
<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a>bd_QC<span class="ot"><-</span><span class="fu">as_tibble</span>(bd_QC) <span class="co">#502,527 </span></span>
<span id="cb9-2"><a href="#cb9-2" aria-hidden="true" tabindex="-1"></a><span class="fu">nrow</span>(bd_QC) <span class="co">#[1] 502527 </span></span></code></pre></div>
<pre><code>## [1] 502527</code></pre>
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a>bd_QC<span class="ot"><-</span>bd_QC<span class="sc">%>%</span><span class="fu">inner_join</span>(pan2, <span class="at">by=</span><span class="st">"IID"</span>)</span></code></pre></div>
</div>
<div id="filter-by-selected-criteria" class="section level3">
<h3>Filter by selected criteria</h3>
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a><span class="co">#Filter by Genetic ethnicity = Caucasian VIA PAN UKBB </span></span>
<span id="cb12-2"><a href="#cb12-2" aria-hidden="true" tabindex="-1"></a>bd_QC<span class="ot"><-</span>bd_QC[bd_QC<span class="sc">$</span>pop<span class="sc">==</span><span class="st">"EUR"</span>,] <span class="co">#nrow(bd_QC) #[1] 426881</span></span>
<span id="cb12-3"><a href="#cb12-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb12-4"><a href="#cb12-4" aria-hidden="true" tabindex="-1"></a>bd_QC<span class="ot"><-</span>bd_QC<span class="sc">%>%</span> <span class="fu">filter</span>(<span class="fu">is.na</span>(Outliers_for_het_or_missing) <span class="sc">|</span> Outliers_for_het_or_missing <span class="sc">!=</span><span class="st">"Yes"</span>) <span class="co">#nrow(bd_QC) #[1] 426433</span></span>
<span id="cb12-5"><a href="#cb12-5" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb12-6"><a href="#cb12-6" aria-hidden="true" tabindex="-1"></a>bd_QC<span class="ot"><-</span>bd_QC<span class="sc">%>%</span> <span class="fu">filter</span>(<span class="fu">is.na</span>(SexchrAneuploidy) <span class="sc">|</span> SexchrAneuploidy <span class="sc">!=</span> <span class="st">"Yes"</span>) <span class="co">#nrow(bd_QC) #[1] 425854</span></span>
<span id="cb12-7"><a href="#cb12-7" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb12-8"><a href="#cb12-8" aria-hidden="true" tabindex="-1"></a>bd_QC<span class="ot"><-</span> bd_QC<span class="sc">%>%</span> <span class="fu">filter</span>(<span class="fu">is.na</span>(Genetic_kinship) <span class="sc">|</span> Genetic_kinship <span class="sc">!=</span> <span class="st">"Ten or more third-degree relatives identified"</span>)</span>
<span id="cb12-9"><a href="#cb12-9" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb12-10"><a href="#cb12-10" aria-hidden="true" tabindex="-1"></a><span class="co">#If Sex does not equal genetic sex, exclude participant </span></span>
<span id="cb12-11"><a href="#cb12-11" aria-hidden="true" tabindex="-1"></a>bd_QC<span class="ot"><-</span>bd_QC[bd_QC<span class="sc">$</span>Sex <span class="sc">==</span> bd_QC<span class="sc">$</span>Genetic_Sex,] </span>
<span id="cb12-12"><a href="#cb12-12" aria-hidden="true" tabindex="-1"></a><span class="fu">nrow</span>(bd_QC) <span class="co">#[1] 425683</span></span></code></pre></div>
<pre><code>## [1] 426373</code></pre>
</div>
<div
id="filter-related-file-by-those-in-qc-from-maximum_set_of_unrelated_individuals.pl1-output"
class="section level3">
<h3>Filter related file by those in QC from
maximum_set_of_unrelated_individuals.pl<a href="#fn1"
class="footnote-ref" id="fnref1"><sup>1</sup></a> output:</h3>
<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb14-1"><a href="#cb14-1" aria-hidden="true" tabindex="-1"></a>max_unrelated<span class="ot"><-</span> <span class="fu">read.table</span>(<span class="st">"src/components/ukb48818_rel_s488282_output.dat"</span>) </span>
<span id="cb14-2"><a href="#cb14-2" aria-hidden="true" tabindex="-1"></a>max_unrelated<span class="ot"><-</span><span class="fu">as.integer</span>(<span class="fu">unlist</span>(max_unrelated)) </span>
<span id="cb14-3"><a href="#cb14-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb14-4"><a href="#cb14-4" aria-hidden="true" tabindex="-1"></a>bd_QC<span class="ot"><-</span>bd_QC<span class="sc">%>%</span><span class="fu">filter</span>(<span class="sc">!</span>IID <span class="sc">%in%</span> max_unrelated)</span>
<span id="cb14-5"><a href="#cb14-5" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb14-6"><a href="#cb14-6" aria-hidden="true" tabindex="-1"></a><span class="fu">table</span>(bd_QC<span class="sc">$</span>pop) <span class="co">#Pan UKBB designation</span></span></code></pre></div>
<pre><code>##
## EUR <NA>
## 357778 0</code></pre>
<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb16-1"><a href="#cb16-1" aria-hidden="true" tabindex="-1"></a><span class="fu">table</span>(bd_QC<span class="sc">$</span>Race) <span class="co">#self identified</span></span></code></pre></div>
<pre><code>##
## Prefer not to answer Do not know
## 872 64
## White Mixed
## 357 4
## Asian or Asian British Black or Black British
## 0 1
## Chinese Other ethnic group
## 1 187
## British Irish
## 342708 7098
## Any other white background White and Black Caribbean
## 6203 4
## White and Black African White and Asian
## 3 16
## Any other mixed background Indian
## 81 2
## Pakistani Bangladeshi
## 0 0
## Any other Asian background Caribbean
## 0 0
## African Any other Black background
## 0 0
## <NA>
## 177</code></pre>
</div>
<div id="save-list-of-participants-for-use-in-future-filtering-steps"
class="section level3">
<h3>Save list of participants for use in future filtering steps</h3>
<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb18-1"><a href="#cb18-1" aria-hidden="true" tabindex="-1"></a>QCkeepparticipants<span class="ot"><-</span>bd_QC<span class="sc">%>%</span><span class="fu">select</span>(IID)</span>
<span id="cb18-2"><a href="#cb18-2" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb18-3"><a href="#cb18-3" aria-hidden="true" tabindex="-1"></a><span class="fu">write.table</span>(QCkeepparticipants, <span class="at">file=</span> <span class="st">"bd_QC-keep.txt"</span>, <span class="at">row.names =</span> <span class="cn">FALSE</span>, <span class="at">quote =</span> <span class="cn">FALSE</span>) </span></code></pre></div>
</div>
<div class="footnotes footnotes-end-of-document">
<hr />
<ol>
<li id="fn1"><p><a href="maxunrelated.html">Max unrelated script</a><a
href="#fnref1" class="footnote-back">↩︎</a></p></li>
</ol>
</div>
</div>
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