reading pgen file into R

Question

[Eliza]

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

[bk11]

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

Answer 1

[chrchang523]

See the pgenlibr package (https://cran.r-project.org/web/packages/pgenlibr/index.html ).