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.
read.bed(bed, bim, fam, only.snp = FALSE)A path of BED file
A path of BIM file
A path of FAM file
If TRUE, the function to read only SNP matrix, otherwise all files are loaded. The default value is FALSE.
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.
For more details about the binary PLINK format, please check http://zzz.bwh.harvard.edu/plink/binary.shtml
#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)
#> [1] "ind.info" "snp" "snp.info"
#Preview $snp
print(snp$snp[1:10, 1:10])
#> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
#> [1,] 0 1 1 1 2 0 1 1 1 2
#> [2,] 1 1 1 2 1 1 1 0 2 2
#> [3,] 2 0 0 1 1 0 1 1 2 2
#> [4,] 2 1 2 2 1 0 1 2 1 2
#> [5,] 2 0 2 2 0 0 1 0 0 1
#> [6,] 2 0 2 0 0 1 2 0 1 2
#> [7,] 1 0 1 2 2 0 0 1 1 2
#> [8,] 2 0 2 2 2 2 0 1 1 2
#> [9,] 2 2 2 1 0 0 0 1 2 1
#> [10,] 2 0 2 1 1 2 1 1 2 2
#Preview $snp.info
head(snp$snp.info)
#> chr ID GD position allele1 allele2
#> 1 1 marker1 0 10000 A T
#> 2 1 marker2 0 20000 A T
#> 3 1 marker3 0 30000 A T
#> 4 1 marker4 0 40000 A T
#> 5 1 marker5 0 50000 A T
#> 6 1 marker6 0 60000 A T
#Preview $ind.info
head(snp$ind.info)
#> FamID IndID PatID MatID sex phenotype
#> 1 1 1 0 0 1 1
#> 2 2 2 0 0 1 1
#> 3 3 3 0 0 1 1
#> 4 4 4 0 0 1 1
#> 5 5 5 0 0 1 1
#> 6 6 6 0 0 1 1