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Table 3 Power and false positive rates of Chi8 and GBOOST on simulated GWAS of 1600 subjects

From: Chi8: a GPU program for detecting significant interacting SNPs with the Chi-square 8-df test

Allele freq. 0.1 0.2 0.4
Model 1
 Chi8 0.22 (0.02) 0.04 (0) 0 (0)
 GBOOST 0.45 (0.12) 0.37 (0.08) 0.09 (0.05)
Model 2
 Chi8 0.22 (0.01) 0.94 (0.02) 0.91 (0.01)
 GBOOST 0.32 (0.09) 0.98 (0.04) 0.98 (0.1)
Model 3
 Chi8 0.25 (0.02) 0.36 (0.02) 0.77 (0)
 GBOOST 0.23 (0.11) 0.49 (0.11) 0.96 (0.06)
Model 4
 Chi8 0.09 (0) 0.73 (0.02) 1 (0.02)
 GBOOST 0.29 (0.08) 0.98 (0.13) 0.98 (0.18)
  1. To account for Chi8’s sensitivity to univariate significant SNPs we only consider reported pairs where both SNPs are also individually insignificant