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Install

install.packages('pgenlibr')

Monthly Downloads

350

Version

0.5.3

License

LGPL (>= 3)

Maintainer

Christopher Chang

Last Published

June 25th, 2025

Functions in pgenlibr (0.5.3)

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.
ReadSparse

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

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

Compute variant scores.
pgenlibr-package

PLINK 2 Binary (.pgen) Reader
GetVariantCt

Returns the number of variants in the file.
GetVariantId

Convert variant index to variant ID string.
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.
NewPvar

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

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

Load hardcalls for multiple variants as an integer matrix.
ReadList

Load dosages for multiple variants as a numeric matrix.
GetVariantsById

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

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

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

Returns the number of samples in the file.
Buf

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

Closes a pvar object, releasing memory.
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.
ClosePgen

Closes a pgen object, releasing resources.
GetMaxAlleleCt

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

Returns whether explicitly phased hardcalls are present.
IntBuf

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

Retrieve chromosome ID for given variant index.
HasSparseHardcalls

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

Look up an allele code.