read.vcf2matrix: Read data of a vcf-file to a matrix
In synbreed: Framework for the Analysis of Genomic Prediction Data using R

Description Usage Arguments Value Author(s) See Also Examples

To easily read genomic data in vcf-Format to a matrix. Function codeGeno uses read.vcf2matrix with imputing by beagle.

read.vcf2matrix(
  file,
  FORMAT = "GT",
  coding = c("allele", "ref"),
  IDinRow = TRUE,
  cores = 1
)

`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.

A matrix (matrix) containing a representation of the data in the file.

Hans-Juergen Auinger

write.vcf, read.vcf2list

## 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)