Table 1. Type 1 error rates of 15 statistics for testing the association of pathway that includes only rare variants with disease.
| Nominal level | |||
|---|---|---|---|
| Test statistics | 0.001 | 0.01 | 0.05 |
| SFPCA | 0.0012 | 0.0106 | 0.0520 |
| FPCA | 0.0012 | 0.0104 | 0.0516 |
| Integral | 0.0008 | 0.0084 | 0.0422 |
| LCT/LCT | 0.0018 | 0.0186 | 0.0742 |
| QT/QT | 0.0016 | 0.0017 | 0.0782 |
| DT/DT | 0.0014 | 0.0132 | 0.0614 |
| WSS/Fisher exact | 0.0016 | 0.0154 | 0.0682 |
| WSS/Sidak | 0.0008 | 0.0096 | 0.0504 |
| WSS/GESA | 0.0008 | 0.0088 | 0.0476 |
| VT/Fisher exact | 0.0014 | 0.0148 | 0.0596 |
| VT/Sidak | 0.0008 | 0.0092 | 0.0498 |
| VT/GESA | 0.0010 | 0.0096 | 0.0486 |
| CMC/Fisher exact | 0.0012 | 0.0118 | 0.0556 |
| CMC/Sidak | 0.0006 | 0.0102 | 0.0508 |
| CMC/GESA | 0.0008 | 0.0106 | 0.0512 |
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.