Simulation analysis.

<p>(A) Histogram of randomly-selected SNPs and highly-selected SNPs, both generated under a null model and uncorrected for multiple testing. The selected SNPs were obtained by taking the most significant SNP from a set of 1,400 null SNPs. The random SNPs were obtained by randomly-selecting a marker from the 198k SNPs. The 200 presented data points were generated from 200 iterations of the simulation. (B) Distribution of −log(<i>P</i>-value) for global likelihood ratio test from the observed method and the permuted method that mimic Lesnick's model selection scheme (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0002707#s4" target="_blank">Materials and Methods</a>). <i>P</i>-values were tallied from 500 observed models and 500 permuted models.