Table 1.

Quantitative traits simulations, average predictive correlation co-efficient (PCC) with standard deviation in parenthesis, average number of true/false positive (TP/FP) results for three methods in replicates. STMGP, smooth-threshold multivariate genetic prediction, Enet, elastic net; GS, gene score. The best performing method is emphasized in bold.

p0	h2		STMGP	Lasso	Enet	GCTA	GS
Oligogenic scenarios (n = 1000)
10	0.13	PCC	0.27 (0.11)	0.28 (0.11)	0.27 (0.11)	0.09 (0.1)	0.1 (0.09)
		TP/FP	3/115	2/46	3/194	-	4/3088
10	0.07	PCC	0.16 (0.12)	0.16 (0.12)	0.16 (0.12)	0.05 (0.1)	0.04 (0.11)
		TP/FP	2/78	1/32	2/133	-	4/7105
50	0.47	PCC	0.55 (0.1)	0.57 (0.09)	0.55 (0.09)	0.27 (0.09)	0.29 (0.1)
		TP/FP	16/509	11/151	19/816	-	20/3488
50	0.31	PCC	0.18 (0.21)	0.17 (0.21)	0.17 (0.2)	0.18 (0.09)	0.19 (0.11)
		TP/FP	5/133	3/50	6/264	-	18/4373
Polygenic scenarios (n = 5000)
100	0.3	PCC	0.46 (0.11)	0.48 (0.11)	0.47 (0.11)	0.28 (0.14)	0.31 (0.1)
		TP/FP	29/904	24/502	36/1073	-	36/2636
100	0.1	PCC	0.23 (0.1)	0.23 (0.11)	0.23 (0.11)	0.11 (0.13)	0.13 (0.14)
		TP/FP	12/257	10/215	17/570	-	30/6413
100	0.05	PCC	0.12 (0.11)	0.13 (0.09)	0.13 (0.11)	0.06 (0.12)	0.05 (0.12)
		TP/FP	6/125	5/129	9/406	-	23/7521
200	0.3	PCC	0.41 (0.09)	0.44 (0.1)	0.43 (0.1)	0.28 (0.09)	0.3 (0.09)
		TP/FP	40/1017	30/434	52/1395	-	54/2726
200	0.1	PCC	0.15 (0.12)	0.17 (0.13)	0.18 (0.12)	0.11 (0.1)	0.11 (0.1)
		TP/FP	13/263	8/140	19/600	-	37/4577
200	0.05	PCC	0.09 (0.1)	0.09 (0.12)	0.1 (0.11)	0.06 (0.11)	0.06 (0.06)
		TP/FP	5/117	4/109	7/300	-	37/7312