Table 4.
Type I error rates and power for Q2 using all SNPs in causal genes
| Model | MAF < 0.005 | 0.005 < MAF < 0.01 | 0.01 < MAF < 0.05 | 0.05 < MAF < 0.5 | Total | |||||
|---|---|---|---|---|---|---|---|---|---|---|
| D (%) | Q (%) | D (%) | Q (%) | D (%) | Q (%) | D (%) | Q (%) | D (%) | Q (%) | |
| Noncausal SNPs | ||||||||||
| SNP | 5.2 | 5.9 | 7.3 | 6.1 | 5.8 | 6.5 | 5.5 | 6.0 | 5.4 | 6.0 |
| Population adjustment | 6.3 | 5.7 | 11.2 | 7.8 | 6.1 | 5.4 | 4.9 | 5.7 | 6.5 | 5.8 |
| PC adjustment | 5.4 | 5.6 | 6.9 | 4.1 | 5.2 | 5.3 | 4.9 | 5.2 | 5.4 | 5.4 |
| Causal SNPs | ||||||||||
| SNP | 11.9 | 13.3 | 30.4 | 31.5 | 39.8 | 45.6 | 55.8 | 80.8 | 16.0 | 18.2 |
| Population adjustment | 11.2 | 12.9 | 31.1 | 29.1 | 39.4 | 46.5 | 48.0 | 70.8 | 15.2 | 17.5 |
| PC adjustment | 11.2 | 12.7 | 26.5 | 24.5 | 36.5 | 44.4 | 45.3 | 69.8 | 14.6 | 16.9 |
D is the dichotomized phenotype; Q is the quantitative phenotype. Nominal type I error rate = 0.05, 200 replicates.