getting bed files into R
I have cleaned up a set of bam files from 64 haploid strains and combined them into vcf files and used plink to extract the unlinked snps. Now I need to extract PCAs; it would be easiest to do this in R since then I will know what I am doing. So my question is how to I go from the bed file into format that I can put into R. I am reluctant to use plink to extract the PCAs as it is set up for diploid data.
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