biCompare-class: Class "biCompare"

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

Description

biCompare class for representing the biCompare results

Slots

method:

Object of class "character". The method to compute the correlated mutations, including ckaksCodon,ckaksAA,miCodon,miAA

state_1:

Object of class "matrix". The conditional kaks(conditional selection pressure) or mutual information among codons or amino mutations.

statistic_1:

Object of class "matrix". LOD confidence score or p value among codons or amino mutations for the first condition.

state_2:

Object of class "matrix". The conditional kaks(conditional selection pressure) or mutual information among codons or amino mutations.

statistic_2:

Object of class "matrix". LOD confidence score or p value among codons or amino mutations for the second condition.

positiveSite01:

Object of class "ANY". A vector of positive selection sites for the first condition.

positiveSite02:

Object of class "ANY". A vector of positive selection sites for the second condition.

Methods

plot

signature(object = "biCompare"): plot the result of biCompare class

See Also

biCompare,plot-methods

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)
#result=biCompare(biexample)

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