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 0.12-12
Index]