4-poissonGWAS.R

# Sample call rate & heterozygosity
callMat <- !is.na(genData$SNP)
Sampstats <- row.summary(genData$SNP)
hetExp <- callMat %*% (2 * SNPstats$MAF * (1 - SNPstats$MAF)) # Hardy-Weinberg heterozygosity (expected)
hetObs <- with(Sampstats, Heterozygosity * (ncol(genData$SNP)) * Call.rate)
Sampstats$hetF <- 1-(hetObs/hetExp)
# Use sample call rate of 100%, het threshold of 0.1 (very stringent)
het <- 0.1 # Set cutoff for inbreeding coefficient;
het_call <- with(Sampstats, abs(hetF) < het & Call.rate == 1)
genData$SNP <- genData$SNP[het_call,]
genData$LIP <- genData$LIP[het_call,]