https://sourceforge.net/p/gbchen/wiki/RealdataSimu/Recent changes to RealdataSimuenMon, 22 Dec 2014 03:15:21 -0000https://sourceforge.net/p/gbchen/wiki/RealdataSimu/<div class="markdown_content"><h2 id="simulation-for-case-control-data-and-quantitative-traits-using-real-gwas-data">Simulation for case-control data and quantitative traits using real GWAS data</h2> <p><strong>Simulating quantitative traits</strong></p> <p>Master option<br /> --bsimu</p> <p><strong>Options</strong><br /> --bfile<br /> Specify the gwas data in binary format</p> <p>--simu-rep<br /> Specify the replication. By default, only 1 replication will be generated.</p> <p>--simu-hsq<br /> Specify the heritability. By defualt, heritability is 0.5.</p> <p>--simu-causal-loci<br /> Specify the file which contains the list for causal snps. One snp per line.</p> <p>--simu-rnd-causal-loci<br /> Alternatively, it can specify the number of causal loci. By default, all markers will be causal, a typical polygenic model.</p> <p>Examples</p> <div class="codehilite"><pre><span class="n">gear</span> <span class="o">--</span><span class="n">bsimu</span> <span class="o">--</span><span class="n">bfile</span> <span class="n">test</span> <span class="o">--</span><span class="n">simu</span><span class="o">-</span><span class="n">rep</span> <span class="mi">10</span> <span class="o">--</span><span class="n">simu</span><span class="o">-</span><span class="n">hsq</span> <span class="mf">0.25</span> <span class="o">--</span><span class="n">simu</span><span class="o">-</span><span class="n">causal</span><span class="o">-</span><span class="n">loci</span> <span class="n">loci</span><span class="p">.</span><span class="n">txt</span> <span class="o">--</span><span class="n">out</span> <span class="n">test</span> <span class="n">gear</span> <span class="o">--</span><span class="n">bsimu</span> <span class="o">--</span><span class="n">bfile</span> <span class="n">test</span> <span class="o">--</span><span class="n">simu</span><span class="o">-</span><span class="n">rep</span> <span class="mi">10</span> <span class="o">--</span><span class="n">simu</span><span class="o">-</span><span class="n">hsq</span> <span class="mf">0.25</span> <span class="o">--</span><span class="n">simu</span><span class="o">-</span><span class="n">rnd</span><span class="o">-</span><span class="n">causal</span><span class="o">-</span><span class="n">loci</span> <span class="mi">100</span> <span class="o">--</span><span class="n">out</span> <span class="n">test</span> </pre></div> </div>Guobo ChenMon, 22 Dec 2014 03:15:21 -0000https://sourceforge.net0f0e24e841f682e59db48d68ae94abbcfeca305d