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Last data update: 2014.03.03

R: Data input

read.bed

R Documentation

Data input

Description

Loads genotype data from plink format files .bed, .bim, and .fam.

Usage

read.bed(bed, bim, fam, sel.snps = NULL, sel.subs = NULL, encode012 = TRUE)

Arguments

`bed`	the name of the bed file.
`bim`	the name of the bim file.
`fam`	the name of the fam file.
`sel.snps`	a character vector of SNPs to be extracted from the plink files. The default is `NULL`, i.e., all SNPs are extracted.
`sel.subs`	an optional character vector specifying a subset of subject IDs to be extracted from the plink files. These IDs should be matched with the second column of `fam` files. The default is `NULL`, i.e., all subjects are extracted.
`encode012`	logical. Encoding the genotypes using 0/1/2 if `TRUE`, or using symbols of the reference and effect alleles if `FALSE`. The default is `TRUE`.

Value

A data frame of genotypes of specified subjects in the plink files.

Examples


# Load the sample data

bed <- system.file("extdata", package = 'ARTP2', 'chr1.bed')
bim <- system.file("extdata", package = 'ARTP2', 'chr1.bim')
fam <- system.file("extdata", package = 'ARTP2', 'chr1.fam')

## first five SNPs
b <- read.table(bim, header = FALSE, as.is = TRUE, nrows = 5)
## first 50 subjects
f <- read.table(fam, header = FALSE, as.is = TRUE, nrows = 50)
geno <- read.bed(bed, bim, fam, sel.snps = b[, 2], sel.subs = f[, 2])

dim(geno) # 50 x 5

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(ARTP2)
Loading required package: Formula
Loading required package: data.table
Loading required package: parallel
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/ARTP2/read.bed.Rd_%03d_medium.png", width=480, height=480)
> ### Name: read.bed
> ### Title: Data input
> ### Aliases: read.bed
> 
> ### ** Examples
> 
> 
> # Load the sample data
> 
> bed <- system.file("extdata", package = 'ARTP2', 'chr1.bed')
> bim <- system.file("extdata", package = 'ARTP2', 'chr1.bim')
> fam <- system.file("extdata", package = 'ARTP2', 'chr1.fam')
> 
> ## first five SNPs
> b <- read.table(bim, header = FALSE, as.is = TRUE, nrows = 5)
> ## first 50 subjects
> f <- read.table(fam, header = FALSE, as.is = TRUE, nrows = 50)
> geno <- read.bed(bed, bim, fam, sel.snps = b[, 2], sel.subs = f[, 2])
> 
> dim(geno) # 50 x 5
[1] 50  5
> 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>