Description Usage Arguments Details Value Author(s) See Also Examples
Create vcf-file for miscellaneous applications. Within the package it is used to write files for beagle usage.
1 |
gp |
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file |
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unphased |
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The function writes a vcf-file. The format of the output is "GT". Other formats are not supported.
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.
Hans-Juergen Auinger
read.vcf2matrix
, read.vcf2list
, codeGeno
1 2 3 4 5 6 7 8 | 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")
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sh: 1: cannot create /dev/null: Permission denied
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