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<h1 class="title toc-ignore">Calculate number of effective
phenotypes</h1>
<h4 class="author">Mike Francis</h4>
<h4 class="date">2022-10-09 21:38:48</h4>
</div>
<p>Calculation for effective number of phenotypes was inspired/borrowed
from here: <a
href="https://github.com/kwesterman/vqtl-gxe/blob/1bc1adb2bc6c46508715279305a92da33620cde1/scripts/6d_ewis_summary.Rmd"
class="uri">https://github.com/kwesterman/vqtl-gxe/blob/1bc1adb2bc6c46508715279305a92da33620cde1/scripts/6d_ewis_summary.Rmd</a></p>
<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">library</span>(tidyverse)</span>
<span id="cb1-2"><a href="#cb1-2" 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">"/Users/mike/Documents/R_files/VegMarkdown/pheno/BioxVeg_pheno_09112022.csv"</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="fu">colnames</span>(tab)</span></code></pre></div>
<pre><code>## [1] "FID" "IID"
## [3] "Age" "Sex"
## [5] "Townsend" "Geno_batch"
## [7] "AlcoholFreq" "Alanine_aminotransferase"
## [9] "Albumin" "Alkaline_phosphatase"
## [11] "Apolipoprotein_A" "Apolipoprotein_B"
## [13] "Aspartate_aminotransferase" "C_reactive_protein"
## [15] "Calcium" "Cholesterol"
## [17] "Creatinine" "Cystatin_C"
## [19] "Direct_bilirubin" "Gamma_glutamyltransferase"
## [21] "Glucose" "HbA1c"
## [23] "HDL_cholesterol" "IGF_1"
## [25] "LDL_direct" "Lipoprotein_A"
## [27] "Oestradiol" "Phosphate"
## [29] "Rheumatoid_factor" "SHBG"
## [31] "Testosterone" "Total_bilirubin"
## [33] "Total_protein" "Triglycerides"
## [35] "Urate" "Urea"
## [37] "Vitamin_D" "PCA1"
## [39] "PCA2" "PCA3"
## [41] "PCA4" "PCA5"
## [43] "PCA6" "PCA7"
## [45] "PCA8" "PCA9"
## [47] "PCA10" "PCA11"
## [49] "PCA12" "PCA13"
## [51] "PCA14" "PCA15"
## [53] "PCA16" "PCA17"
## [55] "PCA18" "PCA19"
## [57] "PCA20" "BMI"
## [59] "SmokeStatus" "Veg5yr1"
## [61] "Age2" "PreviousSmoker"
## [63] "CurrentSmoker" "center1"
## [65] "center2" "center3"
## [67] "center4" "center5"
## [69] "center6" "center7"
## [71] "center8" "center9"
## [73] "center10" "center11"
## [75] "center12" "center13"
## [77] "center14" "center15"
## [79] "center16" "center17"
## [81] "center18" "center19"
## [83] "center20" "center21"
## [85] "center22" "zblood"
## [87] "zTownsend" "zAge"
## [89] "logSHBG" "Scr"
## [91] "eGFR" "bioavailableTest"
## [93] "freeTest" "statins"
## [95] "Cholesterolold" "LDL_directold"
## [97] "Apolipoprotein_Bold" "tookMed"
## [99] "tookSSRI" "Alanine_aminotransferase_rint"
## [101] "Albumin_rint" "Alkaline_phosphatase_rint"
## [103] "Apolipoprotein_A_rint" "Apolipoprotein_B_rint"
## [105] "Aspartate_aminotransferase_rint" "C_reactive_protein_rint"
## [107] "Calcium_rint" "Cholesterol_rint"
## [109] "Creatinine_rint" "Cystatin_C_rint"
## [111] "Direct_bilirubin_rint" "Gamma_glutamyltransferase_rint"
## [113] "Glucose_rint" "HbA1c_rint"
## [115] "HDL_cholesterol_rint" "IGF_1_rint"
## [117] "LDL_direct_rint" "Lipoprotein_A_rint"
## [119] "Oestradiol_rint" "Phosphate_rint"
## [121] "Rheumatoid_factor_rint" "SHBG_rint"
## [123] "Testosterone_rint" "Total_bilirubin_rint"
## [125] "Total_protein_rint" "Triglycerides_rint"
## [127] "Urate_rint" "Urea_rint"
## [129] "Vitamin_D_rint" "eGFR_rint"
## [131] "bioavailableTest_rint" "freeTest_rint"</code></pre>
<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>pheno<span class="ot">=</span>tab<span class="sc">%>%</span><span class="fu">select</span>(Alanine_aminotransferase<span class="sc">:</span>Vitamin_D)<span class="sc">%>%</span><span class="fu">select</span>(</span>
<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a> <span class="sc">-</span><span class="fu">c</span>(Oestradiol, Rheumatoid_factor)</span>
<span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a>)</span>
<span id="cb3-4"><a href="#cb3-4" aria-hidden="true" tabindex="-1"></a><span class="fu">colnames</span>(pheno)</span></code></pre></div>
<pre><code>## [1] "Alanine_aminotransferase" "Albumin"
## [3] "Alkaline_phosphatase" "Apolipoprotein_A"
## [5] "Apolipoprotein_B" "Aspartate_aminotransferase"
## [7] "C_reactive_protein" "Calcium"
## [9] "Cholesterol" "Creatinine"
## [11] "Cystatin_C" "Direct_bilirubin"
## [13] "Gamma_glutamyltransferase" "Glucose"
## [15] "HbA1c" "HDL_cholesterol"
## [17] "IGF_1" "LDL_direct"
## [19] "Lipoprotein_A" "Phosphate"
## [21] "SHBG" "Testosterone"
## [23] "Total_bilirubin" "Total_protein"
## [25] "Triglycerides" "Urate"
## [27] "Urea" "Vitamin_D"</code></pre>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>bm_pca <span class="ot"><-</span> pheno <span class="sc">%>%</span></span>
<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">mutate_all</span>(<span class="sc">~</span><span class="fu">ifelse</span>(<span class="fu">is.na</span>(.), <span class="fu">mean</span>(., <span class="at">na.rm=</span>T), .)) <span class="sc">%>%</span></span>
<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a> <span class="fu">prcomp</span>()</span>
<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a>n_eff_bm <span class="ot"><-</span> <span class="fu">sum</span>(bm_pca<span class="sc">$</span>sdev) <span class="sc">**</span> <span class="dv">2</span> <span class="sc">/</span> <span class="fu">sum</span>(bm_pca<span class="sc">$</span>sdev <span class="sc">**</span> <span class="dv">2</span>)</span>
<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a>n_eff_bm</span></code></pre></div>
<pre><code>## [1] 7.461238</code></pre>
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