kaksAA-class: Class "kaksAA"

In superkits/CorMut: Detect the correlated mutations based on selection pressure

Description

kaksAA class for representing the kaksAA results

Slots

seq_num:

Object of class "list". The number of sequences

kaks:

Object of class "list". kaks value

lod:

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

q:

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

ka:

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

ks:

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

Methods

filterSites

signature(object = "kaksAA"): Filter positive selection amino mutations for objects of kaksAA class.

See Also

filterSites,kaksAA

Examples

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

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