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Table 2 Power and false positive rates of Chi8 and GBOOST on simulated GWAS of 800 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 (0) 0.02 (0.01) 0.01 (0.01)
 GBOOST 0.02 (0.08) 0.01 (0.07) 0 (0.07)
Model 2
 Chi8 0.16 (0) 0.55 (0.01) 0.49 (0)
 GBOOST 0 (0.08) 0.61 (0.07) 0.53 (0.06)
Model 3
 Chi8 0 (0) 0.1 (0.01) 0.18 (0)
 GBOOST 0.01 (0.13) 0.06 (0.06) 0.5 (0.09)
Model 4
 Chi8 0.18 (0) 0.44 (0) 0.55 (0)
 GBOOST 0.01 (0.08) 0.42 (0.11) 0.78 (0.09)
  1. To account for Chi8’s sensitivity to univariate significant SNPs we only consider reported pairs where both SNPs are also individually insignificant