ReadSparseHardcalls: If HasSparseHardcalls() is true, returns a sparse...

In pgenlibr: PLINK 2 Binary (.pgen) Reader

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)

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.

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.

pgenlibr documentation built on June 24, 2025, 1:07 a.m.