Table 2.
Overall false- and true-positive rates for the four rare variant methods (significance level 5%)
| Rare variant method | False-positive rate (%) | True-positive rate (%) | ||||
|---|---|---|---|---|---|---|
| Only SNPs with MAF < 5% | All SNPs | Only nonsynonymous SNPs | Only SNPs with MAF < 5% | All SNPs | Only nonsynonymous SNPs | |
| WS | 9.7 | 10.8 | 9.3 | 15.8 | 18.9 | 14.6 |
| CMAT | 6.9 | 9.2 | 7.8 | 12.3 | 12.8 | 11.6 |
| CMC | 8.9 | 11.2 | 10.1 | 10.6 | 14.3 | 13.9 |
| PR | 6.3 | 8.9 | 7.6 | 12.4 | 13.2 | 10.8 |
All values are averaged over 200 replicates. WS, weighted sum; CMAT, cumulative minor allele test; CMC, combined multivariate and collapsing; PR, proportion regression.