# PLINK 2 Binary (.pgen) Reader

## Documentation for package ‘pgenlibr’ version 0.5.4

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

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.