PLINK dosage data - convert and/or read in R

Question

[Travis]

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.

[Ram]

What have you tried?

Answer 1

[chrchang523]

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

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

[noahpeeri]

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.

[chrchang523]

plink2 exports the original dosages.

[noahpeeri]

Thanks so much