A Two-Stage Penalized Logistic Regression Approach to Case-Control Genome-Wide Association Studies

Table 3

The simulated average PDR and FDR under Model 2: multiplicative effects within loci but not between loci.

(𝑛,𝑃)	𝜆	𝑞	PDR		FDR
			TPLR	MT	TPLR	MT
(800,1000)	0.5	0.1	0.265	0.175	0.086	0.352
	0.5	0.2	0.650	0.550	0.071	0.763
	0.7	0.1	0.790	0.710	0.048	0.758
	0.7	0.2	0.950	1.000	0.050	0.954
(800,5000)	0.5	0.1	0.175	0.085	0.079	0.595
	0.5	0.2	0.610	0.405	0.077	0.928
	0.7	0.1	0.720	0.480	0.062	0.776
	0.7	0.2	0.940	0.930	0.051	0.980