Hi!

I'm trying to make the genotype file from the Illumina EPIC chip using the meffil package.

This is the documentation:

In R:

writeLines(meffil.snp.names(), con="snp-names.txt")

In the UNIX command shell (you will need plink1.90, available here)

plink --bfile dataset --extract snp-names.txt --recode A --out genotypes

In R:

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?