write.vcf {synbreed} | R Documentation |
Create vcf-file for miscellaneous applications. Within the package it is used to write files for beagle usage.
write.vcf(gp, file, unphased = TRUE)
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
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)