reading pgen file into R
Hi,
I downloaded file form here: https://www.cog-genomics.org/plink/2.0/resources#phase3_1kg
The hgdp_chr4.pgen.zst file
I decompressed it to chr4.pfen file but I'm having trouble reading it into R would be happy for your help, tried to make it a bed file but it didn't help:
plink2 --pfile chr4_all.pgen \
--make-bed \
--out chr_4_sim
1 answer
See the pgenlibr package (https://cran.r-project.org/web/packages/pgenlibr/index.html ).
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chrchang523
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Please follow the tutorial in the link below. It will help you what you wanted to accomplish. Please make sure that you are using
Plink2-https://cran.r-project.org/web/packages/snpsettest/vignettes/reference_1000Genomes.html