read.plink {snpMatrix}R Documentation

Read a PLINK binary data file as a snp.matrix

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 creates an object of class "snp.matrix"

Usage

read.plink(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

Value

An object of class "snp.matrix". The column names are the SNP names as listed in the bim file. If the subject identifiers in the fam file are not duplicated, these are used for the row names of the output object. But, if there are duplicated subject identifiers, the row names are generated by concatenating the family and subject identifiers (separated by the character :)

Author(s)

David Clayton david.clayton@cimr.cam.ac.uk

References

~put references to the literature/web site here ~

See Also

read.HapMap.dataread.snps.pedfile, read.snps.chiamo,read.snps.long, snp.matrix-class, X.snp.matrix-class


[Package snpMatrix version 1.6.1 Index]