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PLINK dosage data - convert and/or read in R

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
• 7,630 views • link
updated by noahpeeri • noahpeeri • written by Travis • Travis

What have you tried?

• 1 views • link
written by Ram Ram

1 answer

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

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

• 1 views • link
written by chrchang523 chrchang523

New PLINK user here. Will PLINK automatically apply a hard-call probability threshold to the R-readable form? I am hoping to retrieve the dosage information ranging from 0 --> 2 without applying this probability threshold.

• 0 views • link
written by noahpeeri • noahpeeri

plink2 exports the original dosages.

• 0 views • link
written by chrchang523 chrchang523

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