isVariant {SeqVarTools} | R Documentation

## Locate variant samples across sites

### Description

Locate which samples are variant for each site in a GDS object

### Usage

    ## S4 method for signature 'SeqVarGDSClass'
    isVariant(gdsobj, use.names=FALSE)

### Arguments

`gdsobj` | A `SeqVarGDSClass` object with VCF data.
`use.names` | A logical indicating whether to assign sample and variant IDs as dimnames of the resulting matrix.

### Details

Each sample/site cell of the resulting matrix is `TRUE` if the genotype at that location for that sample contains an alternate allele. A genotype of "0/0" is not variant, while genotypes "0/1", "1/0", "0/2", etc. are variant.

### Value

A logical matrix with dimensions [sample,site] which is `TRUE` for cells where the genotype contains an alternate allele.

### Author(s)

Stephanie Gogarten

### See Also

`SeqVarGDSClass`, `applyMethod`, `getGenotype`

### Examples

    gds <- seqOpen(seqExampleFileName("gds"))
    variant.id <- seqGetData(gds, "variant.id")
    sample.id <- seqGetData(gds, "sample.id")
    applyMethod(gds, isVariant, variant.id[1:5], sample.id[1:10])
    applyMethod(gds, isVariant, variant.id[1:5], sample.id[1:10], use.names=TRUE)
    seqClose(gds)

[Package SeqVarTools version 1.22.0 Index]