calculateTiTv: Calculate transition transversion ratio
In R453Plus1Toolbox: A package for importing and analyzing data from Roche's Genome Sequencer System
Description
Usage
Arguments
Details
Value
Author(s)
Examples
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
1
2
3
4
## 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
1
2
3
data(avaSetExample)
ava = setVariantFilter(avaSetExample, c(0.03, 0.03))
calculateTiTv(ava)
R453Plus1Toolbox documentation built on Nov. 8, 2020, 5:59 p.m.
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Description Usage Arguments Details Value Author(s) Examples
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
1 2 3 4 | ## 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
1 2 3 | data(avaSetExample)
ava = setVariantFilter(avaSetExample, c(0.03, 0.03))
calculateTiTv(ava)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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