Question: PLINK dosage data - convert and/or read in R
1
gravatar for Travis
23 months ago by
Travis10
Travis10 wrote:

I have PLINK dosage files in the form pgen/psam/pvar. I would like to know how to do either/both of the following:

  1. Convert the file set to bed/bim/fam files (hard-calls)

  2. Read the allele dosage from pgen into R as a continuous variable

Thanks.

plink • 1.4k views
ADD COMMENTlink modified 23 months ago by chrchang5237.6k • written 23 months ago by Travis10

What have you tried?

ADD REPLYlink written 23 months ago by _r_am32k
2
gravatar for chrchang523
23 months ago by
chrchang5237.6k
United States
chrchang5237.6k wrote:

Convert to hard-calls: "plink2 --pfile ... --make-bed --out ..."

Convert to an R-readable form: "plink2 --pfile ... --export A-transpose --out ..."

ADD COMMENTlink written 23 months ago by chrchang5237.6k
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