Generate case-control data with shared controls for traits 1 and 2
phen.gen.fn(beta1 = c(-2.3, 0.2, 0.2), beta2 = c(-2.3, 0.2, 0.2), snpG, N0 = 100, N1 = 100, N2 = 100, causals1.ind, causals2.ind)
| beta1 | vector of model parameters for trait 1: (log(prevalence),causal variant effects) |
|---|---|
| beta2 | vector of model parameters for trait 2: (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 |
| causals2.ind | indices of trait 2 causal variants with respect to snpG |
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)