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<title>Phenotype QC</title>
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</head>
<body>
<div class="container-fluid main-container">
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row">
<div class="col-xs-12 col-sm-4 col-md-3">
<div id="TOC" class="tocify">
</div>
</div>
<div class="toc-content col-xs-12 col-sm-8 col-md-9">
<div class="navbar navbar-inverse navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-bs-toggle="collapse" data-target="#navbar" data-bs-target="#navbar">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="index.html">Gene-vegetarianism interactions</a>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="index.html">
<span class="fa fa-home"></span>
Home
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-solid fa-seedling"></span>
Full analysis code
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="DefineVeg.html">
<span class="fa fa-solid fa-seedling"></span>
1a. Define Vegetarians
</a>
</li>
<li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-solid fa-clipboard-check"></span>
1b. Phenotype prep
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="UKB_participantQC.html">
<span class="fa fa-solid fa-user"></span>
Participant QC
</a>
</li>
<li>
<a href="pheno.html">
<span class="fa fa-solid fa-syringe"></span>
Prepare phenotype table
</a>
</li>
<li>
<a href="skim-phenotype.html">
<span class="fa fa-solid fa-list"></span>
Pheno skim
</a>
</li>
</ul>
</li>
<li>
<a href="genoQC.html">
<span class="fa fa-solid fa-filter"></span>
1c. Genotype prep
</a>
</li>
<li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-solid fa-users"></span>
2. Matching + Veg. Effect
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="MatchEffect.html">
<span class="fa fa-solid fa-users"></span>
2. Matching + Veg. Effect
</a>
</li>
<li>
<a href="CompareRaw.html">
<span class="fa fa-regular fa-square"></span>
Compare raw phenotype values
</a>
</li>
</ul>
</li>
<li>
<a href="GWAS.html">
<span class="fa fa-solid fa-dna"></span>
3. Vegetarianism GWAS
</a>
</li>
<li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-solid fa-bolt"></span>
4. Gene x Vegetarianism GWIS
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="GWIS.html">GWIS in GEM</a>
</li>
<li>
<a href="hudson.html">Make interactive Manhattan plots</a>
</li>
</ul>
</li>
<li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-regular fa-folder"></span>
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<h1 class="title toc-ignore">Phenotype QC</h1>
<h4 class="author">Mike Francis</h4>
<h4 class="date">2022-10-09 21:41:24</h4>
</div>
<div
id="prepare-the-phenotype-table-for-biomarker-traits-analyzed-in-this-study."
class="section level1">
<h1>Prepare the phenotype table for biomarker traits analyzed in this
study.</h1>
<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 class="st">"kableExtra"</span>, <span class="st">"DescTools"</span>, <span class="st">"skimr"</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-dataset" class="section level3">
<h3>Load UK Biobank dataset</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></code></pre></div>
</div>
<div id="load-in-second-uk-biobank-dataset" class="section level3">
<h3>Load in second UK Biobank dataset</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><span class="co">#read.lines("src/components/load_UKBphenotables.r") #how I made this file</span></span>
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a>bd_join4<span class="ot"><-</span><span class="fu">vroom</span>(<span class="st">"bd_join4.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="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a>bd_join4<span class="ot">=</span><span class="fu">as_tibble</span>(bd_join4)</span>
<span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a><span class="fu">dim</span>(bd_join4)</span></code></pre></div>
<pre><code>## [1] 501560 2584</code></pre>
</div>
<div id="read-in-extra-files" class="section level3">
<h3>Read in extra files</h3>
<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><span class="fu">source</span>(<span class="st">"src/components/manyColsToDummy.R"</span>)</span>
<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a>hormonemeds<span class="ot"><-</span><span class="fu">read.csv</span>(<span class="st">"src/components/sexHormoneMeds.csv"</span>)</span>
<span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a><span class="fu">source</span>(<span class="st">"src/components/cbat.R"</span>)</span>
<span id="cb6-4"><a href="#cb6-4" aria-hidden="true" tabindex="-1"></a><span class="fu">source</span>(<span class="st">"src/components/SSRI_Meds.R"</span>)</span>
<span id="cb6-5"><a href="#cb6-5" aria-hidden="true" tabindex="-1"></a>codes<span class="ot"><-</span><span class="fu">read.table</span>(<span class="st">"src/components/phenocodes.txt"</span>, <span class="at">header=</span>F)</span>
<span id="cb6-6"><a href="#cb6-6" aria-hidden="true" tabindex="-1"></a>QCids<span class="ot"><-</span><span class="fu">read.table</span>(<span class="st">"src/components/bd_QC-keep.txt"</span>,<span class="at">header=</span><span class="cn">TRUE</span>)</span>
<span id="cb6-7"><a href="#cb6-7" 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="cb6-8"><a href="#cb6-8" aria-hidden="true" tabindex="-1"></a>hormonemeds<span class="sc">%>%</span><span class="fu">kbl</span>()<span class="sc">%>%</span></span>
<span id="cb6-9"><a href="#cb6-9" aria-hidden="true" tabindex="-1"></a> <span class="fu">scroll_box</span>(<span class="at">width =</span> <span class="st">"200px"</span>, <span class="at">height =</span> <span class="st">"200px"</span>)</span></code></pre></div>
<div
style="border: 1px solid #ddd; padding: 0px; overflow-y: scroll; height:200px; overflow-x: scroll; width:200px; ">
<table>
<thead>
<tr>
<th style="text-align:right;position: sticky; top:0; background-color: #FFFFFF;">
code
</th>
<th style="text-align:left;position: sticky; top:0; background-color: #FFFFFF;">
name
</th>
</tr>
</thead>
<tbody>
<tr>
<td style="text-align:right;">
1140869270
</td>
<td style="text-align:left;">
“medroxyprogesterone”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140910674
</td>
<td style="text-align:left;">
“ethinylnortestosterone”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140857656
</td>
<td style="text-align:left;">
“methyltestosterone product”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140865136
</td>
<td style="text-align:left;">
“yohimbine/pemoline/methyltestosterone”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140868532
</td>
<td style="text-align:left;">
“testosterone product”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140857690
</td>
<td style="text-align:left;">
“oestradiol 25mg implant 36 week”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140857700
</td>
<td style="text-align:left;">
“oestradiol 1mg/1ml injection”
</td>
</tr>
<tr>
<td style="text-align:right;">
1141165318
</td>
<td style="text-align:left;">
“cetrorelix”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140917306
</td>
<td style="text-align:left;">
“bicalutamide”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140917310
</td>
<td style="text-align:left;">
“casodex 50mg tablet”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140917448
</td>
<td style="text-align:left;">
“oestradiol 1.25g/dose gel”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140917450
</td>
<td style="text-align:left;">
“oestrogel 1.25g gel”
</td>
</tr>
<tr>
<td style="text-align:right;">
1141171536
</td>
<td style="text-align:left;">
“ganirelix”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140884638
</td>
<td style="text-align:left;">
“clomiphene”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140884634
</td>
<td style="text-align:left;">
“cyproterone”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140870186
</td>
<td style="text-align:left;">
“oestrifen 10mg tablet”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140921100
</td>
<td style="text-align:left;">
“triptorelin”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140868984
</td>
<td style="text-align:left;">
“nafarelin”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140868978
</td>
<td style="text-align:left;">
“gestrinone”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140884544
</td>
<td style="text-align:left;">
“leuprorelin”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140870248
</td>
<td style="text-align:left;">
“buserelin”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140870194
</td>
<td style="text-align:left;">
“goserelin”
</td>
</tr>
<tr>
<td style="text-align:right;">
1141157394
</td>
<td style="text-align:left;">
“goserelin product”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140868882
</td>
<td style="text-align:left;">
“gonadorelin”
</td>
</tr>
<tr>
<td style="text-align:right;">
1141182558
</td>
<td style="text-align:left;">
“urofollitropin”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140868722
</td>
<td style="text-align:left;">
“cyclofenil”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140868580
</td>
<td style="text-align:left;">
“norethisterone”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140869328
</td>
<td style="text-align:left;">
“ethinyloestradiol+norethisterone acetate 20mcg/1mg tablet”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140869356
</td>
<td style="text-align:left;">
“mestranol+norethisterone 50micrograms/1mg tablet”
</td>
</tr>
<tr>
<td style="text-align:right;">
1141157406
</td>
<td style="text-align:left;">
“norethisterone product”
</td>
</tr>
<tr>
<td style="text-align:right;">
1141168324
</td>
<td style="text-align:left;">
“oestradiol+norethisterone acetate 1mg/0.5mg tablet”
</td>
</tr>
<tr>
<td style="text-align:right;">
1141181298
</td>
<td style="text-align:left;">
“ethinylestradiol+norethisterone acetate 20mcg/1mg tablet”
</td>
</tr>
<tr>
<td style="text-align:right;">
1141181204
</td>
<td style="text-align:left;">
“ethinylestradiol+norgestimate 35mcg/250mcg tablet”
</td>
</tr>
<tr>
<td style="text-align:right;">
1141181218
</td>
<td style="text-align:left;">
“ethinylestradiol product”
</td>
</tr>
<tr>
<td style="text-align:right;">
1141181220
</td>
<td style="text-align:left;">
“ethinylestradiol”
</td>
</tr>
<tr>
<td style="text-align:right;">
1141181240
</td>
<td style="text-align:left;">
“ethinylestradiol+levonorgestrel 30mcg/150mcg tablet”
</td>
</tr>
<tr>
<td style="text-align:right;">
1141181286
</td>
<td style="text-align:left;">
“ethinylestradiol+desogestrel 20mcg/150mcg tablet”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140869348
</td>
<td style="text-align:left;">
“ethinyloestradiol+norgestimate 35mcg/250mcg tablet”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140868520
</td>
<td style="text-align:left;">
“estracombi tts patch”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140857628
</td>
<td style="text-align:left;">
“gestone 10mg/1ml injection”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140857704
</td>
<td style="text-align:left;">
“ovestin 250micrograms tablet”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140857706
</td>
<td style="text-align:left;">
“oestriol 250micrograms tablet”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140857708
</td>
<td style="text-align:left;">
“quinestradol”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140857710
</td>
<td style="text-align:left;">
“pentovis 250micrograms tablet”
</td>
</tr>
<tr>
<td style="text-align:right;">
1140857714
</td>
<td style="text-align:left;">
“quinestrol”
</td>