Read .pgen file into R

Source: R/ctwas_read_data.R

Read .pgen file into R

prep_pgen(pgenf, pvarf)

Arguments

pgenf

.pgen file or .bed file

pvarf

.pvar file or .bim file with have proper header. Matching `pgenf`.

Value

A matrix of allele count for each variant (columns) in each sample (rows). ALT allele in pvar file is counted (A1 allele in .bim file is the ALT allele).