setVariantID: Change the variant ID of a GDS file

In smgogarten/SeqVarTools: Tools for variant data

Change the variant ID of a GDS file

Description

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

Usage

setVariantID(gdsfile, variant.id)

Arguments

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

Details

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.

Author(s)

Stephanie Gogarten

See Also

SeqVarGDSClass, seqVCF2GDS

Examples

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)

smgogarten/SeqVarTools documentation built on July 4, 2023, 2:34 a.m.