pgenlibr (version 0.4.0)

pgenlibr-package: PLINK 2 Binary (.pgen) Reader

Description

A thin wrapper over PLINK 2's core libraries which provides an R interface for reading .pgen files. A minimal .pvar loader is also included.

Author

Christopher Chang

Details

NewPvar and NewPgen initialize the respective readers. Then, you can either iterate through one variant at a time (Read, ReadAlleles) or perform a multi-variant matrix load (ReadIntList, ReadList). When you're done, ClosePgen and ClosePvar free resources.

References

Chang, C.C. and Chow, C.C. and Tellier, L.C.A.M. and Vattikuti, S. and Purcell, S.M. and Lee J.J. (2015) Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience 4:7. tools:::Rd_expr_doi("10.1186/s13742-015-0047-8").

Examples

  # This is modified from https://yosuketanigawa.com/posts/2020/09/PLINK2 .
  library(pgenlibr)

  # These files are subsetted from downloads available at
  #   https://www.cog-genomics.org/plink/2.0/resources#phase3_1kg .
  # Note that, after downloading the original files, the .pgen file must be
  # decompressed before use; but both pgenlibr and the PLINK 2 program can
  # handle compressed .pvar files.
  pvar_path <- system.file("extdata", "chr21_phase3_start.pvar.zst", package="pgenlibr")
  pgen_path <- system.file("extdata", "chr21_phase3_start.pgen", package="pgenlibr")

  pvar <- pgenlibr::NewPvar(pvar_path)
  pgen <- pgenlibr::NewPgen(pgen_path, pvar=pvar)

  # Check the number of variants and samples.
  pgenlibr::GetVariantCt(pgen)
  pgenlibr::GetRawSampleCt(pgen)

  # Get the chromosome, position, and ID of the first variant.
  GetVariantChrom(pvar, 1)
  GetVariantPos(pvar, 1)
  GetVariantId(pvar, 1)

  # Read the 14th variant.
  buf <- pgenlibr::Buf(pgen)
  pgenlibr::Read(pgen, buf, 14)

  # Get the index of the variant with ID "rs569225703".
  var_id <- pgenlibr::GetVariantsById(pvar, "rs569225703")

  # Get allele count.
  pgenlibr::GetAlleleCt(pvar, var_id)

  # It has three alleles, i.e. two ALT alleles.
  # Read first-ALT-allele dosages for that variant.
  pgenlibr::Read(pgen, buf, var_id)

  # Read second-ALT-allele dosages.
  pgenlibr::Read(pgen, buf, var_id, allele_num=3)

  # Read a matrix with both variants.  Note that, for the multiallelic variant,
  # the dosages of both ALT alleles are summed here.
  geno_mat <- pgenlibr::ReadList(pgen, c(14, var_id))

  pgenlibr::ClosePgen(pgen)
  pgenlibr::ClosePvar(pvar)