Table 1.

Simulation parameter settings for the single-locus simulations

Item	Parameter	Setting
1	MOI	Dominant, Recessive, Multiplicative
2	ϕ	0.05, 0.15
3	R2	1.0 (Null), 2.25
4	π1	0.25, 0.50, 0.75, 1.0
5	p	0.10, 0.25, 0.50, 0.75, 0.90
6	Number of trios	1000
7	Number of permutations per statistic	500
8	Number of starting points	200
9	Number of EM steps per starting point	100
10	ε	10-6
11	Penalty C in EM algorithm (Equation (1))	0.001
12	Number of replicates per vector (Items 1-3)	250

MOI = Mode of inheritance

ϕ = Disease prevalence

R₂ = Genotype relative risk for disease allele homozygote

π₁ = Proportion of linked trios

p = Disease allele frequency

ε = Tolerance