Extract variants from plink binary

Extract variants from plink binary

Usage

get_pfile_variants(
  snp,
  win_kb,
  chr,
  from_bp,
  to_bp,
  plink2 = genepi.utils::which_plink2(),
  pfile = genepi.utils::which_1000G_reference(build = "GRCh37")
)

Arguments

snp

character, an rsid

win_kb

numeric, window size around snp in kb

chr

character, the chromosome (use instead of snp and win_kb, not in addition)

from_bp

numeric, the start base position (use instead of snp and win_kb, not in addition)

to_bp

numeric, the end base position (use instead of snp and win_kb, not in addition)

plink2

character / path, the plink2 executable

pfile

character / path, the plink pfile set

Value

a data.table