PLINK 2 Binary (.pgen) Reader
Returns an empty two-row numeric matrix that ReadAlleles() can load to...
Returns a bool buffer that ReadAlleles() can load phasing information ...
Returns a numeric buffer that Read() or ReadHardcalls() can load to.
Closes a pgen object, releasing resources.
Closes a pvar object, releasing memory.
Look up an allele code.
Returns the effective number of alleles for a variant. Note that if no...
Returns the maximum GetAlleleCt() value across all variants in the fil...
Returns the number of samples in the file.
Retrieve chromosome ID for given variant index.
Returns the number of variants in the file.
Convert variant index to variant ID string.
Retrieve POS (base-pair coordinate on a chromosome) for given variant ...
Convert variant ID string to variant index(es).
Returns whether explicitly phased hardcalls are present.
Returns whether dosages for the variant_numth variant and given allele...
Returns whether hardcalls for the variant_numth variant and given alle...
Returns an empty two-row integer matrix that ReadAlleles() can load to...
Returns an integer buffer that ReadHardcalls() can load to.
Opens a .pgen or PLINK 1 .bed file.
Loads variant positions, IDs, and allele codes from a .pvar or .bim fi...
PLINK 2 Binary (.pgen) Reader
Loads the variant_numth variant, and then fills buf with numeric dosag...
Loads the variant_numth variant, and then fills acbuf with integer all...
Loads the variant_numth variant, and then fills buf with {0, 1, 2, NA}...
Load hardcalls for multiple variants as an integer matrix.
Load dosages for multiple variants as a numeric matrix.
If HasSparse() is true, returns a sparse representation for the (varia...
If HasSparseHardcalls() is true, returns a sparse representation for t...
Compute variant scores.
A thin wrapper over PLINK 2's core libraries which provides an R interface for reading .pgen files. A minimal .pvar loader is also included. Chang et al. (2015) \doi{10.1186/s13742-015-0047-8}.