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Install

install.packages('pgenlibr')

Monthly Downloads

355

Version

0.4.0

License

LGPL (>= 3)

Maintainer

Christopher Chang

Last Published

January 15th, 2025

Functions in pgenlibr (0.4.0)

GetMaxAlleleCt

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

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

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

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

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

Compute variant scores.
pgenlibr-package

PLINK 2 Binary (.pgen) Reader
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.
ReadList

Load dosages for multiple variants as a numeric matrix.
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.
ReadIntList

Load hardcalls for multiple variants as an integer matrix.
ClosePvar

Closes a pvar object, releasing memory.
GetRawSampleCt

Returns the number of samples in the file.
Buf

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

Returns the number of variants in the file.
GetVariantId

Convert variant index to variant ID string.
GetVariantsById

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

Returns whether explicitly phased hardcalls are present.
GetAlleleCode

Look up an allele code.
GetVariantChrom

Retrieve chromosome ID for given variant index.
NewPvar

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