Table 7:

Simulation for SNP data (n, p) = (300, 505) under banded structures. 50 genes have nonzero regression coefficients. 5 clinical covariates are not subject to selection. The SNPs have Banded.1 (upper panel) or Banded.2 structure (lower panel) with ρ = 0.5. mean(sd) of true positives (TP) and false positives (FP) based on 100 replicates.

		LAD_Network	LAD_MCP	LAD_LASSO	Network	MCP	LASSO
			Banded.1	ρ = 0.5
Error1	TP	39.17(9.57)	36.87(8.19)	30.13(8.40)	31.80(3.95)	26.57(4.39)	43.97(3.18)
	FP	9.10(5.92)	13.53(21.54)	91.63(43.74)	8.27(5.30)	8.53(6.22)	81.93(12.6)
Error2	TP	19.17(9.70)	18.30(13.42)	25.43(8.69)	2.83(7.39)	3.60(9.97)	3.17(5.17)
	FP	14.93(13.16)	57.30(93.44)	97.63(51.97)	17.30(60.78)	24.20(89.50)	13.10(27.14)
Error3	TP	33.33(10.57)	32.47(4.61)	29.97(8.37)	14.60(13.06)	12.83(11.25)	24.40(17.98)
	FP	8.00(4.61)	18.57(38.32)	101.23(52.47)	8.13(7.21)	6.63(6.19)	53.10(37.71)
Error4	TP	33.53(13.54)	29.43(8.05)	31.00(6.77)	11.43(8.63)	10.83(7.73)	24.40(12.76)
	FP	16.37(12.94)	18.30(36.76)	108.90(39.14)	7.07(7.91)	6.53(5.78)	56.57(30.96)
			Banded.2	ρ = 0.5
Error1	TP	41.23(8.78)	40.57(3.30)	34.23(7.57)	32.23(6.74)	27.77(5.10)	45.93(1.76)
	FP	10.83(7.68)	9.17(7.45)	113.63(46.59)	9.63(6.7)	9.30(4.23)	84.00(12.91)
Error2	TP	21.10(7.69)	20.53(13.05)	27.27(8.2)	1.60(1.96)	1.63(2.11)	3.03(4.19)
	FP	17.27(10.43)	76.43(122.77)	93.57(49.76)	5.10(10.5)	5.00(10.3)	11.40(15.40)
Error3	TP	35.60(9.11)	34.90(4.48)	34.20(5.11)	15.30(10.17)	14.37(9.68)	28.67(16.14)
	FP	10.60(7.02)	15.63(38.21)	117.63(38.53)	9.80(7.23)	9.50(7.10)	66.77(37.00)
Error4	TP	38.50(8.44)	36.47(5.17)	33.20(7.07)	12.43(10.86)	11.80(10.26)	21.80(18.26)
	FP	18.77(13.23)	41.57(69.17)	109.73(42.16)	11.13(26.16)	12.90(30.37)	45.90(38.12)