Figure 1.

Evaluation of Covariance Estimation and Statistical Power through Simulations

Detailed simulation settings are described in the Material and Methods.

(A–D) Compare GNOVA and LDSC using traits simulated from a non-stratified covariance structure. We first fixed heritability for both traits but set genetic correlation to different values. The covariance estimates are shown in (A). (B) shows the statistical power. Next, we fixed genetic correlation but chose different values for heritability and covariance. Covariance estimates and statistical power are shown in (C) and (D), respectively.

(E–H) Estimate annotation-stratified genetic covariance. In (E) and (F), we simulated data using two non-overlapping functional annotations. Results in (G) and (H) are based on two overlapping annotations. The true covariance values are labeled under each setting. Type I error was not inflated when the true covariance was zero.