Table 3 Power of different methods in a disease model in which 20% of causal variants are protective
Error rateCoverage per personC-alphaFreq-weightVTRWASLRT_GVSTLRT
040.0540.4170.6530.4710.6460.4560.956
100.0690.460.7120.4720.6890.5060.987
200.070.4730.7130.4780.6990.5150.99
0.0140.0530.140.1640.170.1910.2220.685
100.0660.3040.4680.3760.4950.4250.955
200.060.4580.6730.4650.670.4910.976
  • PAR was 0.02 with ci = 0.1 Tested methods were C-alpha (Neale et al. 2011), Freq-weight similar to the Madsen–Browning method (Madsen and Browning 2009), variable threshold (VT) (Price et al. 2010), RWAS (Sul et al. 2011b), LRT_G (Sul et al. 2011a), and our proposed methods (VST and LRT).