NewPgen {pgenlibr}

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.