read.vcf2matrix {synbreed} | R Documentation |
Read data of a vcf-file to a matrix
Description
To easily read genomic data in vcf-Format to a matrix. Function
codeGeno
uses read.vcf2matrix
with imputing by beagle.
Usage
read.vcf2matrix(
file,
FORMAT = "GT",
coding = c("allele", "ref"),
IDinRow = TRUE,
cores = 1
)
Arguments
file |
character . The name of the file which the data are to be
read from.
|
FORMAT |
character . The default is "GT" . If there are
more formats in your vcf-file you can decide which one you like to have in
your output matrix.
|
coding |
This option has only an effect with FORMAT="GT" .
allele gives you back the alles as defined as REF and ALT in your
vcf-file. ref gives you back "0" for the reference allele and
"1" for the alternative allele.
|
IDinRow |
logical . Default is TRUE , this means the
genotypes are in the rows and the markers in the column. For FALSE it
is the other way round.
|
cores |
numeric . Specifies the number of cores for parallel
computing.
|
Value
A matrix (matrix
) containing a representation of
the data in the file.
Author(s)
Hans-Juergen Auinger
See Also
write.vcf
, read.vcf2list
Examples
## Not run:
library(synbreedData)
data(maize)
maize$info$map.unit <- "kb"
maize <- codeGeno(maize)
write.vcf(maize, "maize.vcf")
geno <- read.vcf2matrix("maize.vcf")
## End(Not run)
[Package
synbreed version 0.12-14
Index]