BEDMatrix-package {BEDMatrix}R Documentation

A Package to Extract Genotypes from a PLINK .bed File


The BEDMatrix package provides a matrix-like wrapper around .bed files, one of the genotype/phenotype file formats of PLINK, the whole genome association analysis toolset. BEDMatrix objects are created by simply providing the path to a .bed file and once created, they behave similarly to regular matrices with the advantage that genotypes are retrieved on demand without loading the entire file into memory. This allows handling of very large files with limited use of memory.

.bed Files

.bed files (sometimes referred to as binary .ped files) are binary representations of genotype calls at biallelic variants. This very compact file format (2 bits per genotype call) is used and generated by PLINK. .bed files should not be confused with the UCSC Genome Browser's BED format, which is totally different.

A .bed file can be created from a .ped file with PLINK using plink --file myfile --make-bed.

See Also

BEDMatrix-class to learn more about the BEDMatrix class.

[Package BEDMatrix version 2.0.3 Index]