Generate case-control data with shared controls for traits 1 and 2, where trait 2 has no associations in this region

Source: R/sims.R

Generate case-control data with shared controls for traits 1 and 2, where trait 2 has no associations in this region

phen.gen.t2null.fn(beta1 = c(-2.3, 0.2, 0.2), snpG, N0 = 100,
  N1 = 100, N2 = 100, causals1.ind)

Arguments

beta1

vector of model parameters for trait 1: (log(prevalence),causal variant effects)
snpG

matrix of genotype scores for null data (rows=SNPs, columns=individuals)
N0

number of shared controls
N1

number of cases for trait 1
N2

number of cases for trait 2
causals1.ind

indices of trait 1 causal variants with respect to snpG

Value

list consisting of G=genotype matrix (rows=indiv, cols=snps), y=vector of case-control status (0=control,1=trait 1 case, 2=trait 2 case)