Figure 1. Permutation -values versus the statistic value on the union-variant .

The mean of the empirical -values (obtained by permuting cases and controls) were plotted against each value of the statistic obtained over many tests over the entire range of simulation parameters, by varying sample size , locus PAR, and penetrance. As is the most significant subset among many possible subsets, the theoretical -value suggested by the distribution cannot be used directly. However, the plot shows that the locus value correlates tightly with the -value, implying that the union statistic can be used to filter the significant windows with no loss of power. The saturation at the ends is due to the number of trial being limited to .