| | | # of variants |
maxH
|
hPDT
|
hPDT-t
|
maxV
|
vPDT
|
vPDT-t
|
---|
Type I error | d%=0 | r%=0 | 21.82(sd=4.63) | 0.053 | 0.050 | 0.035 | 0.045 | 0.052 | 0.041 |
Power | r%=1 | d%=0.5 | 23.02(sd=4.90) | 0.456 | 0.906 | 0.275 | 0.465 | 0.894 | 0.326 |
| | d%=0.4 | 22.63(sd=4.64) | 0.373 | 0.734 | 0.230 | 0.396 | 0.744 | 0.242 |
| | d%=0.3 | 22.65(sd=5.11) | 0.316 | 0.515 | 0.163 | 0.306 | 0.525 | 0.177 |
| | d%=0.2 | 22.31(sd=4.56) | 0.261 | 0.265 | 0.096 | 0.251 | 0.272 | 0.132 |
| | d%=0.1 | 21.89(sd=4.65) | 0.148 | 0.090 | 0.073 | 0.154 | 0.083 | 0.065 |
- Note: (1) “# of variants” indicates the mean and standard deviation (sd) values of the number of SNVs in a 20Kb test region on 1000 replicates (10 permutations for each replicate); (2) d% is the proportion of rare variants in the causal region to be causal; (3) r% is the proportion of causal variants increase risk.
- Abbreviations: maxH: maximal haplotype test; hPDT: haplotype-based pedigree disequilibrium test; hPDT-t: haplotype-based pedigree disequilibrium test with training data; maxV: maximal rare variant test; vPDT: variant-based pedigree disequilibrium test; vPDT-t: rare variant based pedigree disequilibrium test with training data.