ReadHardcalls {pgenlibr}

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.

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

ReadHardcalls(pgen, buf, variant_num, allele_num = 2L)

Arguments

pgen

Object returned by NewPgen().

buf

Buffer returned by Buf() or IntBuf().

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 2.

Value

No return value, called for buf-filling side-effect.