Comparison of Extent of Power Recovery with Missing Genotypes for CERAMIC, CARAT and GMMAT.

<p>Empirical power is based on 10,000 replicates. The error bars indicate 95% confidence intervals. The trait is simulated according to the liability threshold trait model with (<i>π_a</i>, <i>π_b</i>) = (40; 40) with 1,200 individuals in each simulated replicate, under acertainment setting A with missing data. In the “Remove Missing Genotypes” setting, individuals with missing genotypes are removed from the input files before the methods are run. In the “Use Missing Genotypes” setting, individuals with missing genotypes remain in the input files, and GMMAT is run with the option to impute the mean genotype value for the missing genotypes, CERAMIC is run with default settings, and CARAT is run with the mean genotype value plugged in for the missing genotypes in the input file. In the “Complete Genotype Data” setting, the missing genotype values are “unmasked” and included in the input files for all methods.