calculateTiTv {R453Plus1Toolbox} | R Documentation

## Calculate transition transversion ratio

### Description

When many point mutations are detected, the ration of transitions to transversions can be used as quality measure to assess the number of false positives.

### Usage

      ## S4 method for signature 'AVASet'
    calculateTiTv(object)
      ## S4 method for signature 'MapperSet'
    calculateTiTv(object)

### Arguments

`object` | An instance of AVASet or MapperSet storing the detected variants.

### Details

For more information about the Ti/Tv ratio see http://www.broadinstitute.org/gsa/wiki/index.php/QC_Methods

### Value

A `list` with two elements: A substitution matrix summarizing all observed substitutions and the transition/transversion ratio.

### Author(s)

Hans-Ulrich Klein

### Examples

    data(avaSetExample)
    ava = setVariantFilter(avaSetExample, c(0.03, 0.03))
    calculateTiTv(ava)

[Package R453Plus1Toolbox version 1.42.0 Index]