titv {SeqVarTools} | R Documentation

## Transition/Transversion Ratio

### Description

Calculate transition/transversion ratio overall or by sample

### Usage

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

### Arguments

`gdsobj` | A `SeqVarGDSClass` object with VCF data.
`by.sample` | A logical indicating whether TiTv should be calculated by sample or overall for the entire GDS object.
`use.names` | A logical indicating whether to assign sample IDs as names of the output vector (if `by.sample=TRUE`).

### Details

If `by.sample=FALSE` (the default), `titv` calulates the transition/transversion ratio (TiTv) over all samples.

If `by.sample=TRUE`, `titv` calculates TiTv over all variant genotypes (heterozygous or homozygous non-reference) for each sample.

### Value

A single value for TiTv if `by.sample=FALSE`. If `by.sample=TRUE`, a numeric vector containing TiTv for each sample.

### Author(s)

Stephanie Gogarten

### See Also

`SeqVarGDSClass`, `applyMethod`, `isVariant`

### Examples

    gds <- seqOpen(seqExampleFileName("gds"))
    titv(gds)
    titv(gds, by.sample=TRUE)

    ## apply to a subset of variants
    library(GenomicRanges)
    chrom <- seqGetData(gds, "chromosome")
    pos22 <- seqGetData(gds, "position")[chrom == 22]
    ranges <- GRanges(seqnames="22", IRanges(min(pos22), max(pos22)))
    applyMethod(gds, titv, ranges)

    seqClose(gds)

[Package SeqVarTools version 1.30.0 Index]