Table 2.
Type I error rates for Q1 and Q2 using all noncausal SNPs in noncausal 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 (%) | |
| Q1 | ||||||||||
| SNP | 9.7 | 6.0 | 9.0 | 9.3 | 17.0 | 21.2 | 20.9 | 31.3 | 12.1 | 11.7 |
| Population adjustment | 9.1 | 5.8 | 9.0 | 8.5 | 16.3 | 17.9 | 20.0 | 23.6 | 11.5 | 10.0 |
| PC adjustment | 6.6 | 5.7 | 6.3 | 6.4 | 6.8 | 6.9 | 5.7 | 6.7 | 6.5 | 6.0 |
| Q2 | ||||||||||
| SNP | 5.9 | 5.6 | 6.8 | 7.0 | 5.9 | 5.8 | 6.7 | 7.9 | 6.1 | 6.0 |
| Population adjustment | 6.1 | 5.6 | 7.7 | 7.1 | 5.9 | 5.6 | 5.6 | 5.7 | 6.2 | 5.7 |
| PC adjustment | 5.7 | 5.4 | 6.0 | 6.0 | 5.3 | 5.0 | 4.8 | 4.9 | 5.6 | 5.4 |
D is the dichotomized phenotype; Q is the quantitative phenotype. Noncausal SNPs for Q1 come from chromosomes 12, 21, and 22. Noncausal SNPs for Q2 come from chromosomes 21 and 22. Nominal type I error rate = 0.05, 200 replicates.