Skip to content

Instantly share code, notes, and snippets.

Created October 7, 2019 18:51
  • Star 0 You must be signed in to star a gist
  • Fork 0 You must be signed in to fork a gist
Star You must be signed in to star a gist
Save monogenea/98de408819cb19ebb8288617eb98366c to your computer and use it in GitHub Desktop.
# Choose trait for association analysis, use colnames(genData$LIP) for listing
# NOTE: Ignore the first column of genData$LIP (gender)
target <- "Cholesterol"
phenodata <- data.frame("id" = rownames(genData$LIP),
"phenotype" = scale(genData$LIP[,target]), stringsAsFactors = F)
# Conduct GWAS (will take a while)
start <- Sys.time()
GWAA(genodata = genData$SNP, phenodata = phenodata, filename = paste(target, ".txt", sep = ""))
Sys.time() - start # benchmark
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment