readbed: Read the binary PLINK format (BED, BIM, and FAM) efficiently

In danjlawson/pcapred: Produce PC Eigenvector Predictions From Plink Input Data And Loadings

Description

Require the complete set of 3 files in the binary PLINK format. It includes BED file, BIM file and BAM file. For more information about the binary PLINK format, please check in the manual of PLINK.

Reads the binary file into memory but obnly stores binary format; we use accessor functions to

Usage

readbed(bed, bim = NULL, fam = NULL, verbose = TRUE)

Arguments

bed	the file location for the bed file, or the file root
bim	(default NULL, meaning infer from bed) the file location for the bim file, if not using the file root
fam	(default NULL, meaning infer from bed) the file location for the fam file, if not using the file root
verbose	(default TRUE) Whether to report progress

Value

A list containing:

• snp: The SNP matrix loaded from the BED file

• snp.info (if !only.snp) the snp info from the bim file

• ind.info (if !only.snp) the individual info from the fam file

danjlawson/pcapred documentation built on Oct. 7, 2021, 3:47 p.m.