Table 1.

Summary of the objectives and design of simulations 1-3

	Simulation 1	Simulation 2	Simulation 3
Objective	To compare RF VIMs for main and interaction effect detection.	To compare RF measures with p-values from logistic regression for main and interaction effect detection.	Examine RF performance in presence of realistic patterns of LD and MAF.
Independent SNPs	Yes	Yes	No (LD)
# Total Loci (p)	10, 100, 500, 1000	10, 100, 500, 1000	Fixed at 1000
# Causal Loci (k)	4	2	2
MAF	Fixed at 0.1, 0.2, 0.3, or 0.4	Fixed at 0.3	Varies (0.01–0.50)
# Model Scenarios	5	3	4
Description	Varying effect sizes, HX1X22 vs. HX3X42	Two interacting SNPs with 0, 1, or 2 having main effects.	Causal SNPs chosen in blocks of strong vs. weak LD with non-causal SNPs.
Phenotype Generation	Phenotype is a dichotomized quantitative (normally distributed) trait.	Phenotype is based on direct penetrance functions.	Phenotypes are generated as in Simulation 1.