setVariantID {SeqVarTools} | R Documentation

## 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)

[Package SeqVarTools version 1.28.1 Index]