Comparison of epistatic filtration methods with MAPIT and GEMMA on the GEUVADIS data set.

All of these results are based on using MAPIT with genetic relatedness matrix K_cis. (A) shows a histogram of the MAPIT p-values for all variants in the GEUVADIS data set. The horizontal red line corresponds to a uniform distribution of p-values. (B) shows the number of significant pairwise interactions (y-axis) identified by MAPIT (green) and GEMMA (purple) when searching between the top {1000, 2500, 5000, 7500, 10000, 15000, 20000} marginally associated variants (x-axis). We use the number of significant pairs identified by fully exhaustive search model in PLINK as a baseline comparison (orange dotted line). This image shows the distributions of genome-wide significant epistatic pairs as found by each method. An interaction for MAPIT and GEMMA was deemed signifiant if it had a joint p-value below the threshold P = 0.05/(∑_i q_i(q_i − 1)/2), where q_i is the number of top variants located in the cis-window of gene i. In the case of PLINK, we consider two variants to be a significantly associated epistatic pair if they have a joint p-value below the threshold P = 1.09 × 10⁻¹⁰, which corresponds to the Bonferroni-correction that would be used if we examined all possible genome-wide SNP pairs across all genes in the final data set. Overall, PLINK detected 7,361 significant epistatic pairs.