read.plink: Read a PLINK binary data file

Description Usage Arguments Details Value Author(s) References Examples

View source: R/read.plink.R


The package PLINK saves genome-wide association data in groups of three files, with the extensions .bed, .bim, and .fam. This function reads these files and creates a matrix with numeric genotypes and two data frames with information from the .bim, and .fam files.


read.plink(bed, bim, fam, na.strings = c("0", "-9"), sep = "." ,
select.subjects = NULL, select.snps = NULL) 



The name of the file containing the packed binary SNP genotype data. It should have the extension .bed; if it doesn't, then this extension will be appended.


The file containing the SNP descriptions.


The file containing subject (and, possibly, family) identifiers. This is basically a tab-delimited "pedfile".


Strings in .bam and .fam files to be recoded as NA.


A separator character for constructing unique subject identifiers.


A numeric vector indicating a subset of subjects to be selected from the input file (see Details).


Either a numeric or a character vector indicating a subset of SNPs to be selected from the input file (see Details).


If the bed argument does not contain a file name with the file extension .bed, then this extension is appended to the argument. The remaining two arguments are optional; their default values are obtained by replacing the .bed file name extension by .bim and .fam respectively. See the PLINK documentation for the detailed specification of these files.

The select.subjects or select.snps argument can be used to read a subset of the data. Use of select.snps requires that the .bed file is in SNP-major order (the default in PLINK). Likewise, use of select.subjects requires that the .bed file is in individual-major order. Subjects are selected by their numeric order in the PLINK files, while SNPs are selected either by order or by name. Note that the order of selected SNPs/subjects in the output objects will be the same as their order in the PLINK files.

Row names for the output object and for the accompanying subject description data frame are taken as the pedigree identifiers, when these provide the required unique identifiers. When these are duplicated, an attempt is made to use the pedigree-member identifiers instead but, when these too are duplicated, row names are obtained by concatenating, with a separator character, the pedigree and pedigree-member identifiers.


A list with three elements:


The output genotype data as a numeric matrix.


A data frame corresponding to the .fam file, containing the first six fields in a standard pedfile. The row names will correspond with those of the genotype matrix.


A data frame corresponding to the .bim file. the row names correspond with the column names of the genotype matrix.


Originally written by David Clayton (snpStats package), modified by Nadezhda Belonogova


PLINK: Whole genome association analysis toolset.


bedFile <- system.file("testfiles/sample.bed", package = "FREGAT")
data <- read.plink(bedFile)

FREGAT documentation built on Jan. 15, 2018, 9:04 a.m.