Table 4.
Effect of sample size on simulation results for P-value thresholds
| Trait | Threshold (P-value) |
n = 8,816 |
n = 19,840 |
n = 133,653 or 123,865 |
|||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Positives |
eFDRb | Δ sig. loci (% True positive) | Positives |
eFDR | Δ sig. loci (% True positive) |
Positives |
eFDR | Δ sig. loci (% True positive) |
|||||
| False | Truea | False | True | False | True | ||||||||
| Height | 5 × 10-8 | 0.04 | 0.90 | 4.3% | – | 0.03 | 11 | 0.27% | – | 1.6 | 181 | 0.89% | – |
| 5 × 10−7 | 0.40 | 2.2 | 15% | +1.7 (78%) | 0.32 | 18 | 1.7% | +7.4 (96%) | 4.9 | 223 | 2.2% | +46 (93%) | |
| 5 × 10−6 | 3.0 | 5.9 | 34% | +6.3 (58%) | 3.6 | 30 | 11% | +15 (79%) | 16 | 283 | 5.4% | +72 (84%) | |
| BMI | 5 × 10−8 | 0.04 | 0.20 | 17% | – | 0.09 | 1.5 | 5.7% | – | 0.62 | 39 | 1.6% | – |
| 5 × 10−7 | 0.34 | 0.41 | 45% | +0.51 (41%) | 0.46 | 2.4 | 16% | +1.3 (72%) | 2.7 | 58 | 4.4% | +22 (90%) | |
| 5 × 10−6 | 3.1 | 1.2 | 73% | +3.5 (21%) | 3.2 | 4.6 | 41% | +5.0 (44%) | 11 | 90 | 11% | +41 (79%) | |
a
Number of loci in truth set for HDL: 89, LDL: 72, TG: 60, height: 1100, BMI: 724.
b
eFDR is calculated as number of false positives divided by sum of true and false positives.