isSNV {SeqVarTools} | R Documentation

## Flag single nucleotide variants

### Description

Flag single nucleotide variants

### Usage

    ## S4 method for signature 'SeqVarGDSClass'
    isSNV(gdsobj, biallelic=TRUE)

### Arguments

`gdsobj` | A `SeqVarGDSClass` object with VCF data.
`biallelic` | A logical indicating whether only biallelic SNVs are considered.

### Details

If `biallelic=TRUE`, a variant is considered a single nucleotide variant (SNV) if there is one reference allele and one alternate allele, each one base in length. If `biallelic=FALSE`, there may be multiple alternate alleles, each one base in length.

Setting `biallelic=TRUE` is considerably faster for large data sets.

### Value

A logical vector indicating which variants are SNVs.

### Author(s)

Stephanie Gogarten

### See Also

`SeqVarGDSClass`, `allele-methods`, `applyMethod`

### Examples

    gds <- seqOpen(seqExampleFileName("gds"))
    table(isSNV(gds))
    seqClose(gds)

[Package SeqVarTools version 1.28.1 Index]