SNP interaction detection with Random Forests in high-dimensional genetic data

BMC Bioinformatics

Table 2 Simulation 3 results, Model 3

	Level of LD	MAF	Detection Definition	Raw MDA	Liaw MDA	SD MDA	Gini	LR P-value
1	Strong	.294	Causal SNP	0.13	0.12	0.14	0.08	0.21
			Causal Region	0.38	0.3	0.4	0.29	0.49
	Strong	.309	Causal SNP	0.25	0.18	0.28	0.26	0.33
			Causal Region	0.56	0.48	0.55	0.58	0.48
2	Weak	.294	Causal SNP	0.72	0.58	0.73	0.78	0.73
	Weak	.281	Causal SNP	0.66	0.56	0.71	0.79	0.76
3	Strong	.294	Causal SNP	0.15	0.13	0.11	0.08	0.21
			Causal Region	0.5	0.46	0.52	0.39	0.71
	Weak	.294	Causal SNP	0.59	0.52	0.63	0.78	0.5
4	None	.294	Causal SNP	0.67	0.57	0.72	0.73	0.75
	None	.294	Causal SNP	0.68	0.6	0.67	0.7	0.76

Detection probability with and without LD for main effects only Model 3 for RF VIMs and logistic regression (LR). Total number of SNPs = 1,000, MAF ≈ 0.3. Average PE estimates range from 0.458 to 0.477 ( Additional file 2, Table B6).

ISSN: 1471-2105