I'm trying to make the genotype file from the Illumina EPIC chip using the meffil package.
This is the documentation:
In the UNIX command shell (you will need plink1.90, available here)
plink --bfile dataset --extract snp-names.txt --recode A --out genotypes
genotypes <- meffil.extract.genotypes("genotypes.raw") genotypes <- genotypes[,match(samplesheet$Sample_Name, colnames(genotypes))]
However, the files the package want read in is the .idat files and as such I dont have any bed, bim and fam files (bfile format) for plink.
anyone who know how to make the idat files into a bfile format? Or is it another way to do this?