SNP Selection in Genome-Wide Association Studies via Penalized Support Vector Machine with MAX Test

Table 2

The result of simulations with 100 replications: selected SNPs and prognostic SNPs indicate the averaged numbers of the selected SNPs and the selected prognostic SNPs, respectively, in the fitted models; standard error is reported in the parentheses.

𝜌	Genetic model	Selected SNPs			Prognostic SNPs			Misclassification error
		𝑙1	Enet	SCAD	𝑙1	Enet	SCAD	𝑙1	Enet	SCAD
0	Proposed	43.10	48.66	20.31	5.11	5.46	3.31	0.1766	0.1567	0.2736
		(0.54)	(0.70)	(0.65)	(0.09)	(0.07)	(0.14)	(0.0048)	(0.0054)	(0.0062)
	Recessive	40.50	41.38	25.28	4.62	4.74	3.66	0.2408	0.2518	0.2912
		(0.56)	(1.11)	(0.66)	(0.10)	(0.10)	(0.14)	(0.0054)	(0.0065)	(0.0047)
	Additive	42.71	45.58	24.12	5.23	5.35	4.07	0.2161	0.2118	0.3272
		(0.49)	(0.87)	(0.91)	(0.08)	(0.08)	(0.18)	(0.0048)	(0.0064)	(0.0076)
	Dominant	41.35	43.46	23.99	4.70	4.86	3.38	0.2457	0.2347	0.2995
		(0.58)	(0.98)	(0.70)	(0.10)	(0.09)	(0.12)	(0.0056)	(0.0063)	(0.0042)
0.3	Proposed	42.92	45.68	19.56	5.12	5.20	3.40	0.1690	0.1541	0.2833
		(0.50)	(0.80)	(0.48)	(0.08)	(0.08)	(0.10)	(0.0049)	(0.0047)	(0.0060)
	Recessive	39.49	41.09	27.23	4.34	4.47	3.03	0.2383	0.2368	0.2741
		(0.58)	(0.87)	(0.59)	(0.10)	(0.11)	(0.03)	(0.0057)	(0.0057)	(0.0019)
	Additive	42.07	43.90	21.89	5.06	5.04	3.74	0.2126	0.2074	0.3338
		(0.52)	(0.96)	(0.67)	(0.08)	(0.08)	(0.08)	(0.0052)	(0.0057)	(0.0056)
	Dominant	39.97	38.56	24.97	4.56	4.29	2.04	0.2502	0.2338	0.2607
		(0.62)	(1.03)	(0.53)	(0.10)	(0.11)	(0.03)	(0.0065)	(0.0059)	(0.0039)