R453Plus1Toolbox (version 1.22.0)

calculateTiTv: 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

"calculateTiTv"(object) "calculateTiTv"(object)

Arguments

object

An instance of AVASet or MapperSet storing the detected variants.

Value

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

Details

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

Examples

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