LINK output files. The example below uses PLINK to simulate 1000 SNPs, with allele frequencies between 0 and 1 for 100 controls and 0 cases. PhenotypeSimulator::readStandardGenotypes reads the resulting .bim, .fam, .bed files.</p>
<div class="sourceCode"><pre class="sourceCode bash"><code class="sourceCode bash"><span class="co"># Serves as output directory for simulation and parameter file</span>
<span class="fu">mkdir</span> -p ~/PhenotypeSimulator/inst/extdata/genotypes/plink
<span class="bu">cd</span> ~