getPlink {Relate} | R Documentation |
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.
getPlink(bed, bim, fam)
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" |
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().
A list that has the chromosomes, genotypes and positions. The SNP names are stripped.
Anders Albrechtsen albrect@binf.ku.dk
~put references to the literature/web site here ~
path<-paste(.find.package("Relate"),"/data/500",sep="") plinkData<-getPlink(path)