ReadList: Load dosages for multiple variants as a numeric matrix.

In pgenlibr: PLINK 2 Binary (.pgen) Reader

Load dosages for multiple variants as a numeric matrix.

Description

This function treats the data as diploid; divide by 2 to obtain haploid dosages.

Usage

ReadList(pgen, variant_subset, meanimpute = FALSE)

Arguments

pgen	Object returned by NewPgen().
variant_subset	Integer vector containing 1-based indexes of variants to load.
meanimpute	Optional; if true, missing values are mean-imputed instead of being represented by NA.

Value

Numeric matrix, where rows correspond to samples, and columns correspond to variant_subset. Values are in [0, 2] indicating ALT allele dosages, or NA for missing dosages. For multiallelic variants, all ALT alelles are combined.

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