Table 2. Type 1 error rates of 15 statistics for testing the association of pathway that includes all variants with disease.
| Nominal level | |||
|---|---|---|---|
| Test statistics | 0.001 | 0.01 | 0.05 |
| SFPCA | 0.0010 | 0.0102 | 0.0510 |
| FPCA | 0.0012 | 0.0108 | 0.0504 |
| Integral | 0.0008 | 0.0082 | 0.0414 |
| LCT/LCT | 0.0016 | 0.0158 | 0.0638 |
| QT/QT | 0.0016 | 0.0172 | 0.0682 |
| DT/DT | 0.0014 | 0.0120 | 0.0608 |
| WSS/Fisher exact | 0.0014 | 0.0138 | 0.0622 |
| WSS/Sidak | 0.0007 | 0.0092 | 0.0456 |
| WSS/GESA | 0.0008 | 0.0080 | 0.0434 |
| VT/Fisher exact | 0.0014 | 0.0124 | 0.0556 |
| VT/Sidak | 0.0008 | 0.0089 | 0.0458 |
| VT/GESA | 0.0008 | 0.0085 | 0.0440 |
| CMC/Fisher exact | 0.0012 | 0.0102 | 0.0500 |
| CMC/Sidak | 0.0006 | 0.0090 | 0.0454 |
| CMC/GESA | 0.0008 | 0.0104 | 0.0476 |
Abbreviations: CMC, combined multivariate and collapsing; DT, de-correlation test; FPCA, functional principal component analysis; LCT, linear combination test; QT, quadratic test; SFPCA, smoothed functional principal component analysis; VT, variable-threshold; WSS, weighted sum.