synbreed (version 0.11-2)

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)

Arguments

gp

gpData object with elements geno and map

file

character. Filename for writing the file.

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")