Figure 3

Power comparison of genotype-based SKAT, haplotype-based SKAT, MinP-val and SumP-val tests for population genetics simulations, and an estimate of empirical type-1 error. In each panel the top three disease models correspond to the haplotype-based disease scenario, whereas the lower three correspond to the genotype-based scenario. Disease models “Rare”, “Both” and “Common” are described in the section “Population genetics simulation”. Type-1 error is set to 5%. Panel 1: 50% of rare variants/haplotypes were assumed to be causal; Panel 2: 20% of rare variants/haplotypes were assumed to be causal; Panel 3: 10% of rare variants/haplotypes were assumed to be causal; Panel 4: empirical type-1 error estimate for simulations under the null hypothesis.