NewPgen: Opens a .pgen or PLINK 1 .bed file.

In pgenlibr: PLINK 2 Binary (.pgen) Reader

Opens a .pgen or PLINK 1 .bed file.

Description

Opens a .pgen or PLINK 1 .bed file.

Usage

NewPgen(filename, pvar = NULL, raw_sample_ct = NULL, sample_subset = NULL)

Arguments

filename	.pgen/.bed file path.
pvar	Object (see NewPvar()) corresponding to the .pgen's companion .pvar; technically optional, but necessary for some functionality. In particular, at multiallelic variants, all ALT alleles may be collapsed together when .pvar information is not available.
raw_sample_ct	Number of samples in file; required if it's a PLINK 1 .bed file, otherwise optional.
sample_subset	List of 1-based positions of samples to load; optional, all samples are loaded if this is not specified.

Value

A pgen object, which can be queried for genotype/dosage data.

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