Figure 3.

KnockoffTrio prioritizes causal variants over associations due to linkage disequilibrium

(A–C) Comparisons between KnockoffTrio and the conventional method in terms of (A) the proportion of selected windows that overlap with the signal window, (B) the median distance of selected windows to the signal window, and (C) the robustness in controlling false positives in the presence of linkage disequilibrium between causal and non-causal variants. The conventional method is the same aggregated Cauchy association test implemented in KnockoffTrio and controls the FWER using the Bonferroni correction. For KnockoffTrio, the target FDR is 0.1, and the number of multiple knockoffs is 10. The distance in (B) was calculated as the absolute value of the difference between the middle point of a selected window and that of the signal window. The $\left|r\right|$ in (C) is the maximum absolute correlation between the false positive and any causal variants. The variants in the right figure in (C) correspond to the variants in the left figure.