Table 1.
Rejection frequency in 10,000 simulations for 20 high Fst SNPs, under null genetic association
| p value threshold | Expected rejections, n | No adjustment | Known strata | Standard PCA | Shrinkage PCA | Thinning PCA | Regression PCA |
|---|---|---|---|---|---|---|---|
| 10−5 | 2 | 10,000 | 2 | 618 | 24 | 303 | 111 |
| 10−6 | 0.2 | 10,000 | 0 | 142 | 5 | 62 | 21 |
| 5 × 10−7 | 0.1 | 10,000 | 0 | 95 | 1 | 34 | 11 |
| 10−7 | 0.02 | 10,000 | 0 | 29 | 0 | 12 | 0 |
Column 1: The pointwise p value threshold for declaring statistical significance.
Column 2: The expected number of rejections out of 10,000 simulations in which at least one of 20 high Fst SNPs is rejected at a given p value threshold when population stratification is controlled.
Columns 3–8: The observed number of simulations out of 10,000 simulations in which at least one of the 20 high Fst SNPs was rejected at the given p value threshold.