Table 3 Simulation results with MA data using GCTA model with the true heritability \(h^2 = 0.5\)
100 causal SNPs | 5000 causal SNPs | 100 causal SNPs from 3 genes | |
|---|---|---|---|
GCTA | 0.3176 (.0268) | 0.2890 (.0358) | 0.3614 (.0395) |
Enet | 0.4014 (.0393) | 0.4018 (.0538) | 0.3965 (.0474) |
HERRA | 0.5248 (.0342) | 0.5142 (.0586) | 0.5246 (.0427) |
B_herra | 0.5217 (.0260) | 0.5150 (.0447) | 0.5192 (.0339) |
Enet (remove 60% covariates) | 0.4541 (.0364) | 0.4614 (.0371) | 0.4408 (.0403) |
HERRA (remove 60% covariates) | 0.4988 (.0356) | 0.4941 (.0469) | 0.4966 (.0338) |
B_herra (remove 60% covariates) | 0.5015 (.0260) | 0.4892 (.0426) | 0.4965 (.0306) |