read.bed: Reading data from binary PLINK files

In zhangh12/ARTP3: Pathway and Gene-Level Association Test

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. For a SNP without a rs number, use any character (including any white space or '.') in the second column 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. SNPs could be named by its rs number (e.g. rs1234), or by Chr:Pos (e.g. 13:234567, or C13P234567) if a rs number is not available. All other naming methods for a SNP are not accepted in current version.
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, then 2 means two copies of effect allele (6th column of bim file).

Value

A data frame of genotypes of specified subjects in the plink files. For a SNP in sel.snps specified in the format Chr:Pos, e.g. 13:234567, it will be named to be C13P234567 in the returned data frame.

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

zhangh12/ARTP3 documentation built on Aug. 16, 2019, 7:39 p.m.