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pgenlibr (version 0.5.3)

ReadIntList: Load hardcalls for multiple variants as an integer matrix.

Description

This function treats the data as diploid; you can divide by 2, and then treat 0.5 as NA, if it's actually haploid.

Usage

ReadIntList(pgen, variant_subset)

Value

Integer matrix, where rows correspond to samples, columns correspond to variant_subset, and values are in {0, 1, 2, NA} indicating the number of hardcall ALT allele copies. For multiallelic variants, all ALT alleles are combined.

Arguments

pgen

Object returned by NewPgen().

variant_subset

Integer vector containing 1-based indexes of variants to load.