pgenlibr (version 0.5.3)

ReadSparseHardcalls: If HasSparseHardcalls() is true, returns a sparse representation for the (variant, allele) pair. If HasSparseHardcalls() is false, the function fails.

Description

If HasSparseHardcalls() is true, returns a sparse representation for the (variant, allele) pair. If HasSparseHardcalls() is false, the function fails.

Usage

ReadSparseHardcalls(pgen, variant_num, allele_num = 2L, return_ints = FALSE)

Value

An object where "sample_nums" is an increasing sequence of positive integers listing which samples have the allele, and "counts" is a vector listing the allele counts for those samples.

Arguments

pgen

Object returned by NewPgen().

variant_num

Variant index (1-based).

allele_num

Allele index; 1 corresponds to REF, 2 to the first ALT allele, 3 to the second ALT allele if it exists, etc. Optional, defaults to 2.

return_ints

Whether to make the "counts" component of the return value an IntegerVector instead of a NumericVector; defaults to false.