<p>Power was estimated at the nominal level of 5% based on 1,000 replicates. The value of <i>r</i><sup>2</sup> between test and causal sites was set to 1.0, and the recombination rate between the sites was set to 0.01. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0008133#pone-0008133-t001" target="_blank">Table 1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0008133#pone-0008133-t002" target="_blank">2</a> legends for simulation and abbreviation details.</p
<p>True positive rate as a function of false positive rate in simulations with all forty replicate d...
<p>a) A histogram of estimated recombination rates from simulated data under uniform recombination u...
<p>(A) QQ plot of -log10 p values from SNP set tests using different SNP weights under the null simu...
<p>Parents were deleted from the simulation. See <a href="http://www.plosone.org/article/info:doi/10...
<p>Results were based on 200 replicates. In each replicate, 500 cases and 500 controls were used to ...
<p>(<i>N</i> = 5000 “genes”) against the known true correlations used to generate the data (dotted l...
<p>Two hundred nuclear families were simulated, with the number of children per family being drawn f...
<p><i>h</i><sup>2</sup>: variance explained by the locus.</p><p>a: in case-control samples, 50% of t...
<p>In scenario I, only phenotype 1 is associated with the SNP. <i>rG</i> = 1 or −1 does not affect t...
<p>Two hundred nuclear families were simulated by admixing 100 from two populations A and B. See <a ...
<p>A-D, KW, MLM and LM. The “Power” was defined as the detection frequency in 500 repeats for a cert...
<p>The explained variance of the QTL was fixed at 0.1%. For clarity reasons, we have not provided er...
<p>For each dataset, core genes are sorted by increasing GC3 and pooled into 20 classes of equal siz...
<p>Power was measured across one hundred simulations at each of 24 gene loci (as in Figs <a href="ht...
<p>Power of detection for the different 2-locus models. Power was estimated as the proportion of ite...
<p>True positive rate as a function of false positive rate in simulations with all forty replicate d...
<p>a) A histogram of estimated recombination rates from simulated data under uniform recombination u...
<p>(A) QQ plot of -log10 p values from SNP set tests using different SNP weights under the null simu...
<p>Parents were deleted from the simulation. See <a href="http://www.plosone.org/article/info:doi/10...
<p>Results were based on 200 replicates. In each replicate, 500 cases and 500 controls were used to ...
<p>(<i>N</i> = 5000 “genes”) against the known true correlations used to generate the data (dotted l...
<p>Two hundred nuclear families were simulated, with the number of children per family being drawn f...
<p><i>h</i><sup>2</sup>: variance explained by the locus.</p><p>a: in case-control samples, 50% of t...
<p>In scenario I, only phenotype 1 is associated with the SNP. <i>rG</i> = 1 or −1 does not affect t...
<p>Two hundred nuclear families were simulated by admixing 100 from two populations A and B. See <a ...
<p>A-D, KW, MLM and LM. The “Power” was defined as the detection frequency in 500 repeats for a cert...
<p>The explained variance of the QTL was fixed at 0.1%. For clarity reasons, we have not provided er...
<p>For each dataset, core genes are sorted by increasing GC3 and pooled into 20 classes of equal siz...
<p>Power was measured across one hundred simulations at each of 24 gene loci (as in Figs <a href="ht...
<p>Power of detection for the different 2-locus models. Power was estimated as the proportion of ite...
<p>True positive rate as a function of false positive rate in simulations with all forty replicate d...
<p>a) A histogram of estimated recombination rates from simulated data under uniform recombination u...
<p>(A) QQ plot of -log10 p values from SNP set tests using different SNP weights under the null simu...