Table 3 Type I error rates and power for Q1 using all SNPs in causal genes
From: Principal components ancestry adjustment for Genetic Analysis Workshop 17 data
Model | MAF < 0.005 | 0.005 < MAF < 0.01 | 0.01 < MAF < 0.05 | 0.05 < MAF < 0.5 | Total | |||||
|---|---|---|---|---|---|---|---|---|---|---|
| Â | D (%) | Q (%) | D (%) | Q (%) | D (%) | Q (%) | D (%) | Q (%) | D (%) | Q (%) |
Noncausal SNPs | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â |
SNP | 13.5 | 7.8 | 13.8 | 14.4 | 16.9 | 16.7 | 18.4 | 23.6 | 14.5 | 11.1 |
Population adjustment | 11.3 | 7.8 | 10.0 | 11.7 | 15.8 | 14.4 | 8.1 | 9.7 | 11.5 | 9.1 |
PC adjustment | 5.7 | 6.3 | 5.4 | 9.3 | 6.1 | 4.2 | 7.6 | 8.9 | 5.9 | 6.4 |
Causal SNPs | Â | Â | Â | Â | Â | Â | Â | Â | Â | Â |
SNP | 25.6 | 21.4 | NA | NA | 93.1 | 98.2 | 91.8 | 99.3 | 37.6 | 35.2 |
Population adjustment | 22.6 | 21.7 | NA | NA | 91.3 | 97.7 | 85.3 | 98.3 | 34.7 | 35.4 |
PC adjustment | 14.3 | 19.8 | NA | NA | 64.0 | 75.6 | 64.5 | 85.5 | 23.2 | 30.3 |