| BEDMatrix-package {BEDMatrix} | R Documentation |
A Package to Extract Genotypes from a PLINK .bed File
Description
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.