Table 2.
False positive error rates are estimated under the null hypothesis.
| Odds | Sample Sizes | ||||
| Ratios | 250 × 2 | 500 × 2 | 1,000 × 2 | ||
| Null Hypothesis | |||||
| 4.6 | 5.2 | 4.9 | |||
| Alternative Hypothesis with a Single Functional SNP: 0 (ref) and 1 | |||||
| 1.10 | 1.0/1.0/5.8 | 13.6/13.6/6.4 | 23.2/27.9/8.3 | ||
| 1.20 | 13.7/17.2/7.3 | 31.0/37.9/5.5 | 47.2/56.3/6.7 | ||
| 1.30 | 19.0/23.8/4.9 | 46.7/51.6/9.0 | 62.5/75.0/7.3 | ||
| 1.40 | 42.5/44.7/8.0 | 68.5/74.0/6.5 | 75.7/82.0/6.8 | ||
| 1.50 | 57.6/64.4/6.5 | 77.8/80.0/7.0 | 83.0/88.0/6.1 | ||
| 2.00 | 77.0/84.0/6.7 | 90.0/90.8/4.9 | 93.8/93.8/5.6 | ||
| 3.00 | 90.5/92.9/4.8 | 94.8/95.5/6.1 | 96.4/97.0/5.2 | ||
| 5.00 | 92.1/93.5/4.3 | 96.3/96.3/4.9 | 97.5/98.0/5.0 | ||
| Alternative Hypothesis with Two SNPs: 00 (ref), 01, 10 & 11 | |||||
| Scenario 1 | |||||
| 1.0 | 1.3 | 1.0 | 17.6/41.2/7.3 | 42.9/67.8/6.0 | 39.4/71.1/9.0 |
| 1.0 | 1.5 | 1.0 | 30.9/57.1/9.1 | 44.4/76.1/8.0 | 45.9/72.7/10.0 |
| 1.0 | 2.0 | 1.0 | 57.5/90.0/5.3 | 62.2/95.0/4.0 | 79.9/99.3/1.3 |
| 1.0 | 3.0 | 1.0 | 61.2/96.3/4.7 | 63.0/98.0/2.0 | 89.0/99.0/1.0 |
| 1.0 | 5.0 | 1.0 | 64.8/97.8/3.3 | 66.7/99.7/1.4 | 100/100/2.0 |
| Scenario 2 | |||||
| 1.0 | 1.0 | 1.3 | 20.0/46.3/5.0 | 26.1/60.0/6.1 | 30.7/69.2/7.5 |
| 1.0 | 1.0 | 1.5 | 16.7/50.0/4.0 | 23.5/52.9/6.0 | 29.2/78.4/6.5 |
| 1.0 | 1.0 | 2.0 | 10.0/55.6/5.5 | 20.0/66.7/6.5 | 36.0/80.1/6.3 |
| 1.0 | 1.0 | 3.0 | 20.5/74.7/8.0 | 25.7/74.6/6.4 | 34.4/81.0/7.0 |
| 1.0 | 1.0 | 5.0 | 31.6/80.8/9.3 | 32.9/82.1/6.2 | 33.3/85.2/6.0 |
| Scenario 3 | |||||
| 1.0 | 1.3 | 1.3 | 20.8/54.1/7.3 | 21.6/59.5/10.1 | 40.4/67.4/8.1 |
| 1.0 | 1.3 | 1.5 | 22.9/47.6/7.3 | 38.3/78.5/6.0 | 39.5/79.8/8.0 |
| 1.0 | 1.3 | 2.0 | 15.6/48.5/7.6 | 32.0/79.0/6.3 | 44.5/85.3/7.3 |
| 1.0 | 1.3 | 3.0 | 26.7/77.4/6.3 | 38.7/80.1/6.2 | 50.7/91.3/4.6 |
| 1.0 | 1.3 | 5.0 | 30.3/78.7/6.6 | 41.3/82.6/6.0 | 55.5/91.0/4.4 |
| Scenario 4 | |||||
| 1.0 | 1.5 | 1.3 | 44.4/72.2/6.7 | 45.9/79.7/10.0 | 53.3/88.7/7.1 |
| 1.0 | 1.5 | 1.5 | 50.0/75.0/6.6 | 45.7/80.6/9.2 | 47.8/87.3/7.0 |
| 1.0 | 1.5 | 2.0 | 33.9/69.5/9.7 | 37.5/79.4/8.3 | 49.7/93.7/6.3 |
| 1.0 | 1.5 | 3.0 | 28.1/74.6/9.0 | 42.1/82.0/6.7 | 51.0/94.9/6.0 |
| 1.0 | 1.5 | 5.0 | 39.4/86.2/7.7 | 49.2/94.89/5.7 | 53.0/99.4/5.0 |
| Scenario 5 | |||||
| 2.0 | 1.5 | 1.3 | 50.1/82.1/5.3 | 51.9/85.8/7.0 | 56.3/90.1/7.5 |
| 2.0 | 1.5 | 1.5 | 51.7/89.4/7.3 | 52.4/90.0/7.0 | 57.4/93.5/6.7 |
| 2.0 | 1.5 | 2.0 | 52.6/89.3/9.3 | 51.0/92.8/6.3 | 60.0/99.7/5.0 |
| 2.0 | 1.5 | 3.0 | 52.7/89.3/9.0 | 54.1/90.3/6.2 | 65.4/100/4.8 |
| 2.0 | 1.5 | 5.0 | 53.8/89.6/5.3 | 55.3/96.7/5.3 | 70.1/100/4.7 |
Also estimated, under alternative hypotheses with either a single SNP or two SNPs, are the true discovery rate (TDR), imperfect true discovery rate (iTDR) and false positive error rate (FPER).