biCkaksCodon-class: Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA"

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

Description

biCkaksCodon/biCkaksAA/biMICodon/biMIAA class for representing seqFormt result of two conditions

Slots

seq_formated:

Object of class "DNAStringSet". The result of seqFormt for the first condition

seq_formated02:

Object of class "DNAStringSet". The result of seqFormt for the second condition

Methods

biCompare

signature(object = "biCkaksCodon"): Compare the correlated mutations(in the unit of codon) between two conditions using condition kaks method.

biCompare

signature(object = "biCkaksAA"): Compare the correlated mutations(in the unit of amino) between two conditions using condition kaks method.

biCompare

signature(object = "biMICodon"): Compare the correlated mutations(in the unit of codon) between two conditions using mutual information method.

biCompare

signature(object = "biMIAA"): Compare the correlated mutations(in the unit of amino) between two conditions using mutual information method.

See Also

biCompare,plot

Examples

#examplefile=system.file("extdata","PI_treatment_naive.aln",package="CorMut")
#examplefile02=system.file("extdata","PI_treatment.aln",package="CorMut")
#seq_formated=seqFormat(examplefile)
#seq_formated02=seqFormat(examplefile02)
#biexample=biCkaksAA(seq_formated,seq_formated02)

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