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MatchEffect.html
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<title>Match samples and plot Vegetarian effects</title>
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<div class="container-fluid main-container">
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<div class="col-xs-12 col-sm-4 col-md-3">
<div id="TOC" class="tocify">
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</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">
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<h1 class="title toc-ignore">Match samples and plot Vegetarian
effects</h1>
<h4 class="author">Mike Francis</h4>
<h4 class="date">2022-10-09 21:39:36</h4>
</div>
<div id="load-packages-functions" class="section level3">
<h3>Load packages + functions</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">"sandwich"</span>, <span class="st">"lmtest"</span>, <span class="st">"tidyverse"</span>, <span class="st">"MatchIt"</span>, <span class="st">"forestplot"</span>, <span class="st">"kableExtra"</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-phenotype-file" class="section level3">
<h3>Load phenotype file</h3>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a>tab<span class="ot">=</span><span class="fu">as_tibble</span>(<span class="fu">read.csv</span>(<span class="st">"../VegMarkdown/pheno/BioxVeg_pheno_09112022.csv"</span>))</span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="fu">colnames</span>(tab)<span class="sc">%>%</span><span class="fu">kbl</span>()<span class="sc">%>%</span> </span>
<span id="cb2-3"><a href="#cb2-3" 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; ">
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x
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FID
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IID
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Age
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Sex
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Townsend
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Geno_batch
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AlcoholFreq
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Alanine_aminotransferase
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Albumin
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Alkaline_phosphatase
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Apolipoprotein_A
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Apolipoprotein_B
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Aspartate_aminotransferase
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C_reactive_protein
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Calcium
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Cholesterol
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Creatinine
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Cystatin_C
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Direct_bilirubin
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Gamma_glutamyltransferase
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Glucose
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HbA1c
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HDL_cholesterol
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IGF_1
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LDL_direct
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Lipoprotein_A
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Oestradiol
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Phosphate
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Rheumatoid_factor
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SHBG
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Testosterone
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<td style="text-align:left;">
Total_bilirubin
</td>
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Total_protein
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Triglycerides
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Urate
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Urea
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Vitamin_D
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PCA1
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PCA2
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PCA3
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PCA4
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PCA5
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PCA6
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PCA7
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<td style="text-align:left;">
PCA8
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<td style="text-align:left;">
PCA9
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<td style="text-align:left;">
PCA10
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<td style="text-align:left;">
PCA11
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<td style="text-align:left;">
PCA12
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<td style="text-align:left;">
PCA13
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<td style="text-align:left;">
PCA14
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<td style="text-align:left;">
PCA15
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<td style="text-align:left;">
PCA16
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PCA17
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<td style="text-align:left;">
PCA18
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<td style="text-align:left;">
PCA19
</td>
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<td style="text-align:left;">
PCA20
</td>
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<td style="text-align:left;">
BMI
</td>
</tr>
<tr>
<td style="text-align:left;">
SmokeStatus
</td>
</tr>
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<td style="text-align:left;">
Veg5yr1
</td>
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<td style="text-align:left;">
Age2
</td>
</tr>
<tr>
<td style="text-align:left;">
PreviousSmoker
</td>
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<td style="text-align:left;">
CurrentSmoker
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