Step-down inference power simulation over four different configurations of gene signal density.

Simulated power using step-down inference procedure with MAGMA, GSEA, GHC, and GBJ (all self-contained versions) with random sets of ten genes selected from 10,000 total genes. From the ten genes in the set, a genes are selected to hold b causal SNPs each. The four subfigures correspond to (A) a = 1, b = 4, (B) a = 4, b = 1, (C) a = 4, b = 2, (D) a = 8, b = 1. The effect size is given on the x-axis. For each method and each iteration, we first determine a most significant gene. Then that gene is removed and we perform inference on the remaining nine genes in the set. We perform 100 simulations at each parameter setting and test at α = 0.01.