Simulate GRM for small number of SNPs with mother children pairs

grm_sim_duos.R

nsnp <- 48
n <- 1000

mothers1 <- matrix(rbinom(n*nsnp*2, 1, 0.5), n)

kids1 <- matrix(rbinom(n*nsnp, 1, 0.5), n)
kids2 <- mothers1[, seq(1, 2*nsnp, 2)]

kids <- kids1 + kids2

mothers <- matrix(0, n, nsnp)
for(i in 1:nsnp)
{
	mothers[,i] <- mothers1[,(i-1)*2 + 1] + mothers1[,i*2]
}

for(i in 1:10) print(cor(mothers[i,], kids[i,]))


X <- scale(rbind(mothers, kids))

grm <- X %*% t(X) / nsnp / 2

hist(grm[grm > 0.25], breaks=100)
hist(grm)