| # 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 |
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