kaksCodon-class: Class "kaksCodon"

In superkits/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)

superkits/CorMut documentation built on May 8, 2019, 11:59 p.m.