getPlink {Relate}R Documentation

Read a PLINK binary data file as a list of chromosomes, genotypes and positions

Description

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 return a list of chromosomes, positions and genotypes.

Usage

getPlink(bed, bim, fam)

Arguments

bed The name of the file containing the packed binary SNP genotype data
bim The file containing the SNP descriptions
fam The file containing subject (and, possibly, family) identifiers. This is basically a tab-delimited "pedfile"

Details

If the bed argument does not contain a filename 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 filename extension by .bim and .fam respectively. The code is very much inspired by the snpMatrix function called read.plink().

Value

A list that has the chromosomes, genotypes and positions. The SNP names are stripped.

Author(s)

Anders Albrechtsen albrect@binf.ku.dk

References

~put references to the literature/web site here ~

See Also

getPed

Examples


  path<-paste(.find.package("Relate"),"/data/500",sep="")
  plinkData<-getPlink(path)


[Package Relate version 0.987 Index]