calculateTiTv {R453Plus1Toolbox} | R Documentation |
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.
## S4 method for signature 'AVASet' calculateTiTv(object) ## S4 method for signature 'MapperSet' calculateTiTv(object)
object |
An instance of AVASet or MapperSet storing the detected variants. |
For more information about the Ti/Tv ratio see http://www.broadinstitute.org/gsa/wiki/index.php/QC_Methods
A list
with two elements: A substitution matrix summarizing all
observed substitutions and the transition/transversion ratio.
Hans-Ulrich Klein
data(avaSetExample) ava = setVariantFilter(avaSetExample, c(0.03, 0.03)) calculateTiTv(ava)