Table 2.

Performance comparison in simulated data with continuous outcomes

			Shrinkage Parameter
			Approximate test				Permutation test
			0.1	1	10	100	0.1	1	10	100
Individuals	SNPs
500	20
		TPR	1.000	1.000	1.000	1.000	1.000	1.000	1.000	1.000
		FPR	0.045	0.045	0.061	0.133	0.015	0.015	0.017	0.095
	100
		TPR	1.000	1.000	1.000	1.000	1.000	1.000	1.000	1.000
		FPR	0.056	0.054	0.071	0.141	0.015	0.018	0.024	0.074
	1000
		TPR	0.100	0.500	0.900	1.000	0.000	0.200	0.800	1.000
		FPR	0.038	0.045	0.049	0.080	0.007	0.006	0.010	0.029
	ALL
		TPR	1.000	1.000	1.000	1.000	1.000	1.000	1.000	1.000
		FPR	0.318	0.071	0.068	0.069	0.019	0.019	0.020	0.020
1000	20
		TPR	0.900	1.000	1.000	1.000	0.900	1.000	1.000	1.000
		FPR	0.043	0.043	0.087	0.137	0.013	0.013	0.034	0.096
	100
		TPR	0.900	1.000	1.000	1.000	0.900	0.900	1.000	1.000
		FPR	0.051	0.052	0.060	0.108	0.023	0.023	0.019	0.062
	1000
		TPR	0.700	0.700	1.000	1.000	0.400	0.500	0.900	1.000
		FPR	0.060	0.058	0.055	0.076	0.007	0.008	0.010	0.020
	ALL
		TPR	1.000	1.000	1.000	1.000	1.000	1.000	1.000	1.000
		FPR	0.166	0.155	0.110	0.071	0.015	0.015	0.015	0.017
5000	20
		TPR	1.000	1.000	1.000	1.000	1.000	1.000	1.000	1.000
		FPR	0.048	0.048	0.048	0.113	0.006	0.006	0.006	0.053
	100
		TPR	0.900	0.900	1.000	1.000	0.800	0.900	1.000	1.000
		FPR	0.055	0.052	0.062	0.100	0.003	0.001	0.007	0.055
	1000
		TPR	0.700	0.700	1.000	1.000	0.700	0.700	0.900	1.000
		FPR	0.046	0.046	0.045	0.060	0.006	0.007	0.008	0.014
	ALL
		TPR	0.400	0.500	0.900	1.000	0.300	0.900	0.900	1.000
		FPR	0.026	0.027	0.029	0.042	0.007	0.007	0.007	0.009

Performance comparison between a permutation test and the approximate test. Data are simulated genotype data with continuous phenotypes. Reported are proportion of true positive and false positive results at significance threshold α = 0.05. TPR = True Positive Rate, FPR = False positive rate. Results for each simulation scenario are averaged over ten replicates.