Empirical power of exhaustive search procedures to detect epistatic pairs.
Here, the effectiveness of MAPIT (green) as an initial step in a pairwise detection filtration process is compared against the more conventional single-SNP testing procedure, which is carried out via GEMMA (purple). In both cases, the search for epistatic pairs occurs between the top 100 significant marginally associated SNPs are considered. We use the fully exhaustive search model in PLINK (orange) as a baseline comparison. We compare the three methods in all scenarios (x-axis), under broad-sense heritability level H2 = 0.6. Here, ρ = 0.8 was used to determine the portion of broad-sense heritability contributed by interaction effects. The y-axis gives the rate at which true causal epistatic pairs were identified. Results are based on 100 replicates in each case. The lines represent 95% variability due to resampling error.
