Table 4.
Type I error rates for the IGOF tests in the presence of LD or population stratification at the 1% significance level.
| No. of variantsa | IGOFcommon | IGOFLF | IGOFcombined | |
|---|---|---|---|---|
| LD | ||||
| Strong | 50,50 (38,47) | 0.0100 | 0.0124 | 0.011 |
| Weak | 50,50 (36,41) | 0.0086 | 0.0094 | 0.0076 |
| STRATIFICATION | ||||
| AFR:800b | 50,50 (43,45) | 0.0058 | 0 | 0.0026 |
| EUR:3200 | ||||
| AFR:2000 | 50,50 (43,45) | 0.0048 | 0 | 0.0022 |
| EUR:2000 | ||||
| AFR:3200 | 50,50 (43,45) | 0.0046 | 0 | 0.0010 |
| EUR:800 | ||||
a
Number of variants in the two genes and the numbers in parentheses show the numbers of variants with MAFs < 1%.
b
Sample sizes in each population. The numbers of cases and controls are equal.