PLINK 2 Binary (.pgen) Reader

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Documentation for package ‘pgenlibr’ version 0.4.0

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pgenlibr-package PLINK 2 Binary (.pgen) Reader
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.
Buf Returns a numeric buffer that Read() or ReadHardcalls() can load to.
ClosePgen Closes a pgen object, releasing resources.
ClosePvar Closes a pvar object, releasing memory.
GetAlleleCode Look up an allele code.
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.
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.
GetVariantId Convert variant index to variant ID string.
GetVariantPos Retrieve POS (base-pair coordinate on a chromosome) for given variant index.
GetVariantsById Convert variant ID string to variant index(es).
HardcallPhasePresent Returns whether explicitly phased hardcalls are present.
IntAlleleCodeBuf Returns an empty two-row integer matrix that ReadAlleles() can load to.
IntBuf Returns an integer buffer that ReadHardcalls() can load to.
NewPgen Opens a .pgen or PLINK 1 .bed file.
NewPvar Loads variant positions, IDs, and allele codes from a .pvar or .bim file (which can be compressed with gzip or Zstd).
pgenlibr PLINK 2 Binary (.pgen) Reader
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.
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.
ReadIntList Load hardcalls for multiple variants as an integer matrix.
ReadList Load dosages for multiple variants as a numeric matrix.
VariantScores Compute variant scores.