PLINK 2 Binary (.pgen) Reader

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Documentation for package ‘pgenlibr’ version 0.5.3

• DESCRIPTION file.
• Package NEWS.

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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.
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.
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.
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.
ReadSparse	If HasSparse() is true, returns a sparse representation for the (variant, allele) pair. If HasSparse() is false, the function fails.
ReadSparseHardcalls	If HasSparseHardcalls() is true, returns a sparse representation for the (variant, allele) pair. If HasSparseHardcalls() is false, the function fails.
VariantScores	Compute variant scores.