File S1 - SNP Set Association Analysis for Genome-Wide Association Studies

Figure S1, Test powers at single causal SNP model based on 100 SNPs. The plot shows the powers (y-axis) of each method over the different LD and MAF structures (x-axis). The first line of x-axis represents LD, and the bottom line is MAF. Figure S2, Test powers at two causal SNPs model based on 100 SNPs. The plot shows the powers (y-axis) of each method over the different LD and MAF structures (x-axis). The first line of x-axis represents LD, and the bottom line is MAF. Table S1, Empirical type I error rates at the significance level of 0.01based on 10 SNPs. Table S2, Empirical type I error rates at the significance level of 0.001 based on 10 SNPs. Table S3, Empirical type I error rates at the significance level of 0.01based on 100 SNPs. Table S4, Empirical type I error rates at the significance level of 0.001 based on 100 SNPs. Table S5, Test power at the significance level of 0.05 for four methods in Scenarios B10-B11. Table S6, Test power at the significance level of 0.05 for four methods in Scenarios C3–C4. Table S7, Run time comparison. (DOCX)