read.plink {snpMatrix} | 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 creates an object of
class "snp.matrix"
read.plink(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
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 :
)
David Clayton david.clayton@cimr.cam.ac.uk
~put references to the literature/web site here ~
read.HapMap.data
read.snps.pedfile
,
read.snps.chiamo
,read.snps.long
,
snp.matrix-class
, X.snp.matrix-class