ReadAlleles: Loads the variant_numth variant, and then fills acbuf with...

In pgenlibr: PLINK 2 Binary (.pgen) Reader

Loads the variant_numth variant, and then fills acbuf with integer allele codes, where each column of the buffer corresponds to a sample. An allele code of 0 corresponds to the REF allele, 1 to the first ALT, 2 to the second ALT, etc. Missing hardcalls are represented by a pair of NA codes.

Description

This function treats the data as diploid. If it's really haploid, you may want to compare the two rows, and then treat samples where the allele codes differ as missing values.

Usage

ReadAlleles(pgen, acbuf, variant_num, phasepresent_buf = NULL)

Arguments

pgen	Object returned by NewPgen().
acbuf	Buffer returned by AlleleCodeBuf() or IntAlleleCodeBuf().
variant_num	Variant index (1-based).
phasepresent_buf	Buffer returned by BoolBuf(). Optional; if provided, elements are set to true when the sample has known phase. Most of these values will be TRUE even when the raw data is unphased, because homozygous genotypes always have known phase. (Missing genotypes are considered to have unknown phase.)

Value

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

pgenlibr documentation built on April 3, 2025, 6:21 p.m.