read.bed: Read the binary PLINK format (BED, BIM, and FAM)
In KRIS: Keen and Reliable Interface Subroutines for Bioinformatic Analysis

Description Usage Arguments Details Value See Also Examples

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.

1	read.bed(bed, bim, fam, only.snp = FALSE)

`bed`	A path of BED file
`bim`	A path of BIM file
`fam`	A path of FAM file
`only.snp`	If TRUE, the function to read only SNP matrix, otherwise all files are loaded. The default value is FALSE.

For more details about the binary PLINK format, please check http://zzz.bwh.harvard.edu/plink/binary.shtml

The list containing the matrices of $snp, $snp.info, and $ind.info.

$snp is a SNP matrix from BED file.
$snp.info is a data.frame of SNP information from BIM file.
$ind.info is a data.frame of individual information from FAM file.

write.bed

#Use the example files embedded in the package.
bed <- system.file("extdata", "example_SNP.bed", package="KRIS")
bim <- system.file("extdata", "example_SNP.bim", package="KRIS")
fam <- system.file("extdata", "example_SNP.fam", package="KRIS")
snp <- read.bed(bed, bim, fam )

#Check the objects inside 'snp'
ls(snp)

#Preview $snp
print(snp$snp[1:10, 1:10])

#Preview $snp.info
head(snp$snp.info)

#Preview $ind.info
head(snp$ind.info)