Table 1 Power of different methods, on 1000 data sets and a region with 100 rare SNVs
Error rateCoverage per personC-alphaFreq-weightVTRWASLRT_GVSTLRT
040.0620.6590.8720.6680.8170.9730.975
100.0620.7130.9030.6880.8540.980.99
200.0670.7220.9030.6920.8580.9870.988
0.0140.0510.1740.2080.2690.2860.6340.745
100.0660.4790.6740.6100.710.9650.972
200.0670.6860.8870.6900.8480.9880.993
  • Two error rates (0% and 1%) were considered with three different coverages (4, 10, and 20). Population attributable risk of the region was 0.02, with ci = 0.1 and a significance threshold of 0.05. 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).