write.vcf: Prepare genotypic data in vcf-Format

In synbreed: Framework for the Analysis of Genomic Prediction Data using R

Description

Create vcf-file for miscellaneous applications. Within the package it is used to write files for beagle usage.

Usage

write.vcf(gp, file, unphased = TRUE)

Arguments

gp	gpData object with elements geno and map
file	character. Filename for writing the file.
unphased	logical. The default is TRUE. Than the seperator between the alleles is "/", and the possible codings are "0/0" for 0 in the genotype matrix, "0/1" for 1 and "1/1" for 2. For getting a phased output, use unphased=FALSE. Than the seperator is "|". For hetercygous genotypes you have to change the 1 to -1 if you like to get the coding "1|0", So posible codings in this case are "0|0" for 0 in the genotype matrix, "0|1" for 1, "1|0" for -1 and "1|1" for 2.

Details

The function writes a vcf-file. The format of the output is "GT". Other formats are not supported.

Value

No value is returned. Function creates files [prefix]ingput.bgl with genotypic data in Beagle input format and [prefix]marker.txt with marker information used by Beagle.

Author(s)

Hans-Juergen Auinger

See Also

read.vcf2matrix, read.vcf2list, codeGeno

Examples

map <- data.frame(chr = c(1, 1, 1, 1, 1, 2, 2, 2, 2), pos = 1:9)
geno <- matrix(sample(c(0, 1, 2, NA), size = 10 * 9, replace = TRUE), nrow = 10, ncol = 9)
colnames(geno) <- rownames(map) <- paste("SNP", 1:9, sep = "")
rownames(geno) <- paste("ID", 1:10 + 100, sep = "")

gp <- create.gpData(geno = geno, map = map)
gp1 <- discard.markers(gp, rownames(map[map$chr != 1, ]))
## Not run: 
write.vcf(gp1, file = "test.vcf")

## End(Not run)

synbreed documentation built on March 12, 2021, 3:01 a.m.