allele-methods {SeqVarTools} | R Documentation

## Extract allele information from a GDS object

### Description

Extract reference and alternate alleles and allele counts from a GDS object.

### Usage

    ## S4 method for signature 'SeqVarGDSClass'
    refChar(gdsobj)
    ## S4 method for signature 'SeqVarGDSClass'
    altChar(gdsobj, n=0)
    ## S4 method for signature 'SeqVarGDSClass'
    nAlleles(gdsobj)

### Arguments

`gdsobj` | A `SeqVarGDSClass` object with VCF data.
`n` | An integer indicating which alternate allele to return. `n=0` returns a comma-separated string of all alternate alleles.

### Details

These methods parse the "allele" field of a GDS object.

### Value

`refChar` returns a character vector of reference alleles.

`altChar` returns a character vector of alternate alleles. If `n=0`, multiple alternate alleles are represented as a comma-separated string. If `n>0`, only the `n`th alternate allele is returned.

`nAlleles` returns an integer vector of the number of alleles (reference and alternate) for each variant.

### Author(s)

Stephanie Gogarten

### See Also

`SeqVarGDSClass`, `applyMethod`

### Examples

    gds <- seqOpen(seqExampleFileName("gds"))
    table(refChar(gds))
    table(altChar(gds))
    table(altChar(gds, n=1))
    table(altChar(gds, n=2), useNA="ifany")
    table(nAlleles(gds))
    seqClose(gds)

[Package SeqVarTools version 1.28.1 Index]