kaksCodon-class: Class "kaksCodon"

In CorMut: Detect the correlated mutations based on selection pressure

Description

kaksCodon class for representing the kaksCodon results

Slots

seq_num:

Object of class "list". The number of sequences

kaks:

Object of class "numeric". kaks value

lod:

Object of class "numeric". LOD confidence score, refer to vignette for details

q:

Object of class "numeric". q value, refer to vignette for details

ka:

Object of class "numeric".ka value of kaks ratio, i.e. the samples count of the nonsynonymous mutation.

ks:

Object of class "numeric". ks value of kaks ratio, i.e. the samples count of the synonymous mutation.

Methods

filterSites

signature(object = "kaksCodon"): Filter positive selection sites for objects of kaksCodon class.

See Also

kaksCodon,filterSites

Examples

#examplefile=system.file("extdata","PI_treatment.aln",package="CorMut")
#example=seqFormat(examplefile)
#result=kaksCodon(example)

Example output

Loading required package: seqinr
Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

CorMut documentation built on April 28, 2020, 7:09 p.m.