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<h1 class="title toc-ignore">Prep GWIS summary statistics</h1>
<h4 class="author">Mike Francis</h4>
<h4 class="date">2022-10-09 22:11:17</h4>
</div>
<p>Put the GEM output files into GWAS catalog summary statistics
format.</p>
<p>Only keep robust-SE-associated values.</p>
<div class="sourceCode" id="cb1"><pre
class="sourceCode bash"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="ex">suppressMessages</span><span class="er">(</span><span class="ex">library</span><span class="er">(</span><span class="ex">tidyverse</span><span class="kw">))</span></span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="ex">library</span><span class="er">(</span><span class="ex">vroom</span><span class="kw">)</span></span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="va">pheno</span><span class="op">=</span>c<span class="kw">(</span><span class="st">"Alanine_aminotransferase_rint"</span><span class="ex">,</span> <span class="st">"Albumin_rint"</span>, <span class="st">"Alkaline_phosphatase_rint"</span>, </span>
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="st">"Apolipoprotein_A_rint"</span><span class="ex">,</span> <span class="st">"Apolipoprotein_B_rint"</span>, <span class="st">"Aspartate_aminotransferase_rint"</span>, </span>
<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="st">"C_reactive_protein_rint"</span><span class="ex">,</span> <span class="st">"Calcium_rint"</span>, <span class="st">"Cholesterol_rint"</span>,<span class="st">"Creatinine_rint"</span>, <span class="st">"Cystatin_C_rint"</span>, </span>
<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a><span class="st">"Direct_bilirubin_rint"</span><span class="ex">,</span> <span class="st">"Gamma_glutamyltransferase_rint"</span>, </span>
<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a><span class="st">"HbA1c_rint"</span><span class="ex">,</span> <span class="st">"HDL_cholesterol_rint"</span>, <span class="st">"IGF_1"</span>, <span class="st">"LDL_direct_rint"</span>, </span>
<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a><span class="st">"Lipoprotein_A_rint"</span><span class="ex">,</span> <span class="st">"Phosphate_rint"</span>, <span class="st">"SHBG_rint"</span>, <span class="st">"Testosterone_rint"</span>,</span>
<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a><span class="st">"Total_bilirubin_rint"</span><span class="ex">,</span> <span class="st">"Total_protein_rint"</span>, </span>
<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a><span class="st">"Triglycerides_rint"</span><span class="ex">,</span> <span class="st">"Urate_rint"</span>, <span class="st">"Urea_rint"</span>, <span class="st">"Vitamin_D_rint"</span>, </span>
<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a><span class="st">"eGFR_rint"</span><span class="ex">,</span> <span class="st">"freeTest_rint"</span>, <span class="st">"bioavailableTest_rint"</span><span class="kw">)</span></span>
<span id="cb1-13"><a href="#cb1-13" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-14"><a href="#cb1-14" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-15"><a href="#cb1-15" aria-hidden="true" tabindex="-1"></a><span class="va">exp</span><span class="op">=</span><span class="st">"Veg5yr1"</span></span>
<span id="cb1-16"><a href="#cb1-16" aria-hidden="true" tabindex="-1"></a><span class="va">dir</span><span class="op">=</span><span class="st">"/scratch/mf91122/BioxVeg/gem5"</span></span>
<span id="cb1-17"><a href="#cb1-17" aria-hidden="true" tabindex="-1"></a><span class="va">dirb</span><span class="op">=</span><span class="st">"/scratch/mf91122/BioxVeg/gem5-BMI"</span></span>
<span id="cb1-18"><a href="#cb1-18" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-19"><a href="#cb1-19" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-20"><a href="#cb1-20" aria-hidden="true" tabindex="-1"></a><span class="ex">outdir</span><span class="op"><</span>-paste<span class="er">(</span><span class="fu">dir</span>, <span class="st">"/summary"</span>, sep=<span class="st">""</span><span class="kw">)</span></span>
<span id="cb1-21"><a href="#cb1-21" aria-hidden="true" tabindex="-1"></a><span class="ex">suppressWarnings</span><span class="er">(</span><span class="ex">dir.create</span><span class="er">(</span><span class="ex">outdir</span><span class="kw">))</span></span>
<span id="cb1-22"><a href="#cb1-22" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-23"><a href="#cb1-23" aria-hidden="true" tabindex="-1"></a><span class="cf">for</span> <span class="kw">(</span><span class="ex">i</span> in 1:length<span class="er">(</span><span class="ex">pheno</span><span class="kw">)){</span> <span class="co">#loop over phenotypes</span></span>
<span id="cb1-24"><a href="#cb1-24" aria-hidden="true" tabindex="-1"></a><span class="ex">print</span><span class="er">(</span><span class="fu">paste</span><span class="er">(</span><span class="st">"running "</span> , pheno[i]<span class="kw">))</span></span>
<span id="cb1-25"><a href="#cb1-25" aria-hidden="true" tabindex="-1"></a><span class="fu">file</span><span class="op"><</span>-list<span class="er">(</span><span class="kw">)</span></span>
<span id="cb1-26"><a href="#cb1-26" aria-hidden="true" tabindex="-1"></a><span class="cf">for</span> <span class="kw">(</span><span class="ex">c</span> in 1:22<span class="kw">){</span></span>
<span id="cb1-27"><a href="#cb1-27" aria-hidden="true" tabindex="-1"></a> <span class="va">file</span><span class="op">[</span>[c<span class="op">]</span><span class="ex">]</span><span class="op"><</span>-as_tibble<span class="er">(</span><span class="ex">vroom</span><span class="er">(</span></span>
<span id="cb1-28"><a href="#cb1-28" aria-hidden="true" tabindex="-1"></a> <span class="fu">paste</span><span class="er">(</span><span class="fu">dir</span>,<span class="st">"/"</span>, pheno[i], <span class="st">"/chr"</span>, c, sep=<span class="st">""</span><span class="kw">)</span><span class="ex">,</span> show_col_types = FALSE<span class="kw">))</span></span>
<span id="cb1-29"><a href="#cb1-29" aria-hidden="true" tabindex="-1"></a><span class="kw">}</span></span>
<span id="cb1-30"><a href="#cb1-30" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-31"><a href="#cb1-31" aria-hidden="true" tabindex="-1"></a><span class="fu">file</span><span class="op"><</span>-do.call<span class="er">(</span><span class="ex">rbind,</span> file<span class="kw">)</span></span>
<span id="cb1-32"><a href="#cb1-32" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-33"><a href="#cb1-33" aria-hidden="true" tabindex="-1"></a><span class="ex">fileb</span><span class="op"><</span>-list<span class="er">(</span><span class="kw">)</span></span>
<span id="cb1-34"><a href="#cb1-34" aria-hidden="true" tabindex="-1"></a><span class="cf">for</span> <span class="kw">(</span><span class="ex">c</span> in 1:22<span class="kw">){</span></span>
<span id="cb1-35"><a href="#cb1-35" aria-hidden="true" tabindex="-1"></a> <span class="va">fileb</span><span class="op">[</span>[c<span class="op">]</span><span class="ex">]</span><span class="op"><</span>-as_tibble<span class="er">(</span><span class="ex">vroom</span><span class="er">(</span></span>
<span id="cb1-36"><a href="#cb1-36" aria-hidden="true" tabindex="-1"></a> <span class="fu">paste</span><span class="er">(</span><span class="ex">dirb,</span><span class="st">"/"</span><span class="ex">,</span> pheno[i], <span class="st">"/chr"</span>, c, sep=<span class="st">""</span><span class="kw">)</span><span class="ex">,</span> show_col_types = FALSE<span class="kw">))</span></span>
<span id="cb1-37"><a href="#cb1-37" aria-hidden="true" tabindex="-1"></a><span class="kw">}</span></span>
<span id="cb1-38"><a href="#cb1-38" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-39"><a href="#cb1-39" aria-hidden="true" tabindex="-1"></a><span class="ex">fileb</span><span class="op"><</span>-do.call<span class="er">(</span><span class="ex">rbind,</span> fileb<span class="kw">)</span></span>
<span id="cb1-40"><a href="#cb1-40" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-41"><a href="#cb1-41" aria-hidden="true" tabindex="-1"></a><span class="ex">colnames</span><span class="er">(</span><span class="fu">file</span><span class="kw">)</span><span class="ex">=c</span><span class="er">(</span><span class="st">"SNPID"</span><span class="ex">,</span> <span class="st">"variant_ID"</span>, <span class="st">"chromosome"</span>, <span class="st">"base_pair_location"</span>, </span>
<span id="cb1-42"><a href="#cb1-42" aria-hidden="true" tabindex="-1"></a><span class="st">"other_allele"</span><span class="ex">,</span> <span class="st">"effect_allele"</span>, <span class="st">"N"</span>, <span class="st">"effect_allele_frequency"</span>, <span class="st">"N_nonveg"</span>, </span>
<span id="cb1-43"><a href="#cb1-43" aria-hidden="true" tabindex="-1"></a><span class="st">"effect_allele_frequency_nonveg"</span><span class="ex">,</span> <span class="st">"N_veg"</span>, <span class="st">"effect_allele_frequency_veg"</span>, </span>
<span id="cb1-44"><a href="#cb1-44" aria-hidden="true" tabindex="-1"></a><span class="st">"beta_marginal"</span><span class="ex">,</span> <span class="st">"robust_SE_beta_marginal"</span>, <span class="st">"SE_beta_marginal"</span>, <span class="st">"beta_mainG"</span>, </span>
<span id="cb1-45"><a href="#cb1-45" aria-hidden="true" tabindex="-1"></a><span class="st">"beta_interaction"</span><span class="ex">,</span> <span class="st">"robust_SE_beta_mainG"</span>, <span class="st">"robust_SE_beta_interaction"</span>, </span>
<span id="cb1-46"><a href="#cb1-46" aria-hidden="true" tabindex="-1"></a><span class="st">"robust_Cov_main_int"</span><span class="ex">,</span> <span class="st">"SE_beta_mainG"</span>, <span class="st">"SE_beta_interaction"</span>, </span>
<span id="cb1-47"><a href="#cb1-47" aria-hidden="true" tabindex="-1"></a><span class="st">"Cov_main_int"</span><span class="ex">,</span> <span class="st">"robust_p_value_Marginal"</span>,<span class="st">"p_value"</span>,<span class="st">"robust_p_value_joint"</span>,</span>
<span id="cb1-48"><a href="#cb1-48" aria-hidden="true" tabindex="-1"></a><span class="st">"P_Value_Marginal"</span><span class="ex">,</span><span class="st">"P_Value_Interaction"</span><span class="ex">,</span><span class="st">"P_Value_Joint"</span><span class="kw">)</span></span>
<span id="cb1-49"><a href="#cb1-49" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-50"><a href="#cb1-50" aria-hidden="true" tabindex="-1"></a><span class="va">file</span><span class="op">=</span>file%<span class="op">></span>%select<span class="kw">(</span><span class="ex">variant_ID:robust_SE_beta_marginal,</span> beta_mainG:robust_Cov_main_int, </span>
<span id="cb1-51"><a href="#cb1-51" aria-hidden="true" tabindex="-1"></a> <span class="ex">robust_p_value_Marginal:robust_p_value_joint</span><span class="kw">)</span></span>
<span id="cb1-52"><a href="#cb1-52" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-53"><a href="#cb1-53" aria-hidden="true" tabindex="-1"></a><span class="ex">write.table</span><span class="er">(</span><span class="fu">file</span>, paste<span class="er">(</span><span class="st">"/scratch/mf91122/BioxVeg/gem5/summary/noBMI/"</span><span class="ex">,</span> pheno[i], <span class="st">".txt"</span>, sep=<span class="st">""</span><span class="kw">)</span><span class="ex">,</span></span>
<span id="cb1-54"><a href="#cb1-54" aria-hidden="true" tabindex="-1"></a> <span class="va">quote</span><span class="op">=</span>F, <span class="ex">row.names=F,</span> fileEncoding=<span class="st">"ascii"</span><span class="kw">)</span></span>
<span id="cb1-55"><a href="#cb1-55" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-56"><a href="#cb1-56" aria-hidden="true" tabindex="-1"></a><span class="ex">colnames</span><span class="er">(</span><span class="ex">fileb</span><span class="kw">)</span><span class="ex">=c</span><span class="er">(</span><span class="st">"SNPID"</span><span class="ex">,</span> <span class="st">"variant_ID"</span>, <span class="st">"chromosome"</span>, <span class="st">"base_pair_location"</span>,</span>
<span id="cb1-57"><a href="#cb1-57" aria-hidden="true" tabindex="-1"></a><span class="st">"other_allele"</span><span class="ex">,</span> <span class="st">"effect_allele"</span>, <span class="st">"N"</span>, <span class="st">"effect_allele_frequency"</span>, <span class="st">"N_nonveg"</span>,</span>
<span id="cb1-58"><a href="#cb1-58" aria-hidden="true" tabindex="-1"></a><span class="st">"effect_allele_frequency_nonveg"</span><span class="ex">,</span> <span class="st">"N_veg"</span>, <span class="st">"effect_allele_frequency_veg"</span>,</span>
<span id="cb1-59"><a href="#cb1-59" aria-hidden="true" tabindex="-1"></a><span class="st">"beta_marginal"</span><span class="ex">,</span> <span class="st">"robust_SE_beta_marginal"</span>, <span class="st">"SE_beta_marginal"</span>, <span class="st">"beta_mainG"</span>,</span>
<span id="cb1-60"><a href="#cb1-60" aria-hidden="true" tabindex="-1"></a><span class="st">"beta_interaction"</span><span class="ex">,</span> <span class="st">"robust_SE_beta_mainG"</span>, <span class="st">"robust_SE_beta_interaction"</span>,</span>
<span id="cb1-61"><a href="#cb1-61" aria-hidden="true" tabindex="-1"></a><span class="st">"robust_Cov_main_int"</span><span class="ex">,</span> <span class="st">"SE_beta_mainG"</span>, <span class="st">"SE_beta_interaction"</span>,</span>
<span id="cb1-62"><a href="#cb1-62" aria-hidden="true" tabindex="-1"></a><span class="st">"Cov_main_int"</span><span class="ex">,</span> <span class="st">"robust_p_value_Marginal"</span>,<span class="st">"p_value"</span>,<span class="st">"robust_p_value_joint"</span>,</span>
<span id="cb1-63"><a href="#cb1-63" aria-hidden="true" tabindex="-1"></a><span class="st">"P_Value_Marginal"</span><span class="ex">,</span><span class="st">"P_Value_Interaction"</span><span class="ex">,</span><span class="st">"P_Value_Joint"</span><span class="kw">)</span> </span>
<span id="cb1-64"><a href="#cb1-64" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-65"><a href="#cb1-65" aria-hidden="true" tabindex="-1"></a><span class="va">fileb</span><span class="op">=</span>fileb%<span class="op">></span>%select<span class="kw">(</span><span class="ex">variant_ID:robust_SE_beta_marginal,</span> beta_mainG:robust_Cov_main_int,</span>
<span id="cb1-66"><a href="#cb1-66" aria-hidden="true" tabindex="-1"></a> <span class="ex">robust_p_value_Marginal:robust_p_value_joint</span><span class="kw">)</span></span>
<span id="cb1-67"><a href="#cb1-67" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-68"><a href="#cb1-68" aria-hidden="true" tabindex="-1"></a><span class="ex">write.table</span><span class="er">(</span><span class="ex">fileb,</span> paste<span class="er">(</span><span class="st">"/scratch/mf91122/BioxVeg/gem5/summary/adjBMI/"</span><span class="ex">,</span> pheno[i], <span class="st">".txt"</span>, sep=<span class="st">""</span><span class="kw">)</span><span class="ex">,</span></span>
<span id="cb1-69"><a href="#cb1-69" aria-hidden="true" tabindex="-1"></a> <span class="va">quote</span><span class="op">=</span>F, <span class="ex">row.names=F,</span> fileEncoding=<span class="st">"ascii"</span><span class="kw">)</span></span>
<span id="cb1-70"><a href="#cb1-70" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb1-71"><a href="#cb1-71" aria-hidden="true" tabindex="-1"></a><span class="kw">}</span></span></code></pre></div>
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