This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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,] |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment