I am working on a genome-wide association study. I wish to examine the time to onset of a disease in relation to the alleles present at each SNP (survival analysis). I have done this for a few snps using STATA, but this won't work for a whole genome dataset so I am trying to do it in R.
My files are in PLINK format, and I have included the time to event data in the fam section of the read in plink data using the merge command.
My script is below:
#Read in plink files GWAS<-read.plink("R.bed","R.bim","R.fam") pheno <- read.delim("C:/Users/USER/Desktop/pheno.txt") view(pheno) library("GenABEL", lib.loc="~/R/win-library/3.1") #find columns head(GWAS) #merge plink file with followup and presence of disease GWAS$fam <-merge(GWAS$fam,pheno, by.x="member", by.y= "Chip") #this is now included in the plink files #running in cox model using GenABEL package and mlreg command coxm <- mlreg(GWAS((fam$followup),(map$allele.1)),"fam$disease")
However, it's not working, I'm pretty new at this and I'm not sure how to specify the genotype at each snp for each individual. Has anyone ran a genome-wide cox model in R? If so help would be greatly appreciated!