setVariantID: Change the variant ID of a GDS file
In SeqVarTools: Tools for variant data

Description Usage Arguments Details Author(s) See Also Examples

Replace the variable "variant.id" in a GDS file with a user-supplied unique vector of the same length.

1	setVariantID(gdsfile, variant.id)

`gdsfile`	A character string with the file path of a GDS file.
`variant.id`	A vector with the new variant IDs.

A VCF file created by seqVCF2GDS creates a variable "variant.id" containing sequential integers to identify each variant. setVariantID allows the user to replace these values with something more meaningful. The replacement values in variant.id must be unique and have the same length as the original "variant.id" vector.

Using character values for variant.id may affect performance for large datasets.

Stephanie Gogarten

SeqVarGDSClass, seqVCF2GDS

oldfile <- system.file("extdata", "gl_chr1.gds", package="SeqVarTools")
newfile <- tempfile()
file.copy(oldfile, newfile)

gds <- seqOpen(newfile)
rsID <- seqGetData(gds, "annotation/id")
seqClose(gds)

setVariantID(newfile, rsID)
gds <- seqOpen(newfile)
seqGetData(gds, "variant.id")
head(getGenotype(gds))
seqClose(gds)
 
unlink(newfile)