synbreed (version 0.11-22)

write.vcf: Prepare genotypic data in vcf-Format

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"

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.

Details

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

See Also

read.vcf2matrix, 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,]))
write.vcf(gp1,prefix="test")