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Version

Install

install.packages('pgenlibr')

Monthly Downloads

498

Version

0.5.2

License

LGPL (>= 3)

Maintainer

Christopher Chang

Last Published

June 23rd, 2025

Functions in pgenlibr (0.5.2)

ClosePvar

Closes a pvar object, releasing memory.
ReadIntList

Load hardcalls for multiple variants as an integer matrix.
pgenlibr-package

PLINK 2 Binary (.pgen) Reader
HardcallPhasePresent

Returns whether explicitly phased hardcalls are present.
VariantScores

Compute variant scores.
Read

Loads the variant_numth variant, and then fills buf with numeric dosages in [0, 2] indicating the dosages of the first ALT (or user-specified) allele for each sample, with missing values represented by NA.
ClosePgen

Closes a pgen object, releasing resources.
GetAlleleCode

Look up an allele code.
IntBuf

Returns an integer buffer that ReadHardcalls() can load to.
GetRawSampleCt

Returns the number of samples in the file.
GetVariantChrom

Retrieve chromosome ID for given variant index.
GetVariantCt

Returns the number of variants in the file.
ReadList

Load dosages for multiple variants as a numeric matrix.
NewPgen

Opens a .pgen or PLINK 1 .bed file.
HasSparse

Returns whether dosages for the variant_numth variant and given allele are represented in a sparse manner that is supported by ReadSparse(), under the current sample subset.
NewPvar

Loads variant positions, IDs, and allele codes from a .pvar or .bim file (which can be compressed with gzip or Zstd).
ReadHardcalls

Loads the variant_numth variant, and then fills buf with {0, 1, 2, NA} values indicating the number of copies of the first ALT (or user-specified) allele each sample has.
GetVariantId

Convert variant index to variant ID string.
ReadAlleles

Loads the variant_numth variant, and then fills acbuf with integer allele codes, where each column of the buffer corresponds to a sample. An allele code of 0 corresponds to the REF allele, 1 to the first ALT, 2 to the second ALT, etc. Missing hardcalls are represented by a pair of NA codes.
GetAlleleCt

Returns the effective number of alleles for a variant. Note that if no pvar was provided to the NewPgen() call, this function may return 2 even at multiallelic variants, since the .pgen may not store allele-count information.
GetMaxAlleleCt

Returns the maximum GetAlleleCt() value across all variants in the file.
Buf

Returns a numeric buffer that Read() or ReadHardcalls() can load to.
GetVariantPos

Retrieve POS (base-pair coordinate on a chromosome) for given variant index.
ReadSparse

If HasSparse() is true, returns a sparse representation for the (variant, allele) pair. If HasSparse() is false, the function fails.
AlleleCodeBuf

Returns an empty two-row numeric matrix that ReadAlleles() can load to.
BoolBuf

Returns a bool buffer that ReadAlleles() can load phasing information to.
ReadSparseHardcalls

If HasSparseHardcalls() is true, returns a sparse representation for the (variant, allele) pair. If HasSparseHardcalls() is false, the function fails.
GetVariantsById

Convert variant ID string to variant index(es).
HasSparseHardcalls

Returns whether hardcalls for the variant_numth variant and given allele are represented in a sparse manner that is supported by ReadSparseHardcalls().
IntAlleleCodeBuf

Returns an empty two-row integer matrix that ReadAlleles() can load to.