Table III.
Empirical false positive rates across simulation replicates for gene-wise testing at Bonferroni corrected α = 0.05 (0.05/597 ≈ 8.38e-05) for all simulation scenarios and methods.
| Scenario | Methods
|
||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| EB-SGL | EB-SGL (no sing) | GB-L | GB-L (no sing) | SKAT | SKAT-O | WSS | C-alpha | CAST | |||
|
| |||||||||||
| Causal Variant % | OR model | Causal variants | |||||||||
| 40 | Fixed | Random | 5.92e-04 | 6.40e-04 | 3.00e-04 | 3.44e-04 | 5.85e-05 | 6.22e-05 | 1.06e-04 | 5.69e-03 | 4.02e-05 |
| Exon | 6.29e-04 | 7.64e-04 | 3.07e-04 | 2.89e-04 | 2.92e-05 | 6.94e-05 | 1.39e-04 | 5.78e-03 | 5.11e-05 | ||
| Var. | Random | 4.79e-04 | 7.17e-04 | 2.63e-04 | 1.83e-04 | 2.55e-05 | 4.75e-05 | 1.06e-04 | 5.48e-03 | 2.92e-05 | |
| Exon | 7.50e-04 | 5.78e-04 | 1.79e-04 | 2.05e-04 | 6.21e-05 | 6.94e-05 | 1.57e-04 | 5.70e-03 | 6.58e-05 | ||
|
| |||||||||||
| 20 | Fixed | Random | 6.69e-04 | 5.78e-04 | 2.82e-04 | 2.27e-04 | 6.94e-05 | 7.31e-05 | 2.05e-04 | 5.86e-03 | 8.41e-05 |
| Exon | 5.81e-04 | 5.78e-04 | 3.55e-04 | 2.52e-04 | 6.94e-05 | 7.67e-05 | 1.54e-04 | 5.94e-03 | 4.75e-05 | ||
| Var. | Random | 7.09e-04 | 5.74e-04 | 3.25e-04 | 3.22e-04 | 4.39e-05 | 8.04e-05 | 1.90e-04 | 6.00e-03 | 5.12e-05 | |
| Exon | 8.00e-04 | 6.00e-04 | 4.13e-04 | 3.95e-04 | 5.85e-05 | 9.51e-05 | 1.83e-04 | 5.98e-03 | 6.94e-05 | ||