Description Usage Arguments Details Value Note Author(s) References See Also
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 "SnpMatrix"
1 | read.plink(bed, bim, fam, na.strings = c("0", "-9"), sep = "." , select.subjects = NULL, select.snps = NULL)
|
bed |
The name of the
file containing the packed binary SNP genotype data. It should have
the extension |
bim |
The file containing the SNP descriptions |
fam |
The file containing subject (and, possibly, family) identifiers. This is basically a tab-delimited "pedfile" |
na.strings |
Strings in .bam and .fam files to be recoded as NA |
sep |
A separator character for constructing unique subject identifiers |
select.subjects |
A numeric vector indicating a subset of subjects to be selected from the input file (see details) |
select.snps |
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 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. 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.snps
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 SnpMatrix
object and for the
accompanying subject description dataframe 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:
genotypes |
The output genotype data as an object of class |
"SnpMatrix"
.
fam |
A dataframe corresponding to the |
map |
A dataframe correponding to the |
No special provision is made to read XSnpMatrix
objects; such data should first be read as a SnpMatrix
and then
coerced to an XSnpMatrix
using new
or as
.
David Clayton dc208@cam.ac.uk
PLINK: Whole genome association analysis toolset. http://pngu.mgh.harvard.edu/~purcell/plink/
write.plink
,
SnpMatrix-class
, XSnpMatrix-class
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.