biCompare-methods: biCompare implement biCompare methods for comparison of the...

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

Description

Comparison of the correlated mutations between two conditions by the means of correlated mutation network, two correlated mutation network will be displayed in a plot, which represent the global mutation correlation among sites or mutations in two conditions. In the plot, blue nodes indicate the positive selection nodes in the first condition, while red nodes indicate the positive selection nodes in the second condition.

Value

A biCompare instance is returned.

Methods

x = "biCkaksCodon"

Compare the correlated mutations(in the unit of codon) between two conditions using condition kaks method.

x = "biCkaksAA"

Compare the correlated mutations(in the unit of amino) between two conditions using condition kaks method.

x = "biMICodon"

Compare the correlated mutations(in the unit of codon) between two conditions using mutual information method.

x = "biMIAA"

Compare the correlated mutations(in the unit of amino) between two conditions using mutual information method.

x = "biJIAA"

Compare the correlated mutations(in the unit of amino) between two conditions using mutual information method.

Author(s)

Zhenpeng Li

See Also

biCompare-class,plot.biCompare

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)
#biexample=biCkaksCodon(seq_formated,seq_formated02)
#biexample=biMIAA(seq_formated,seq_formated02)
#biexample=biMICodon(seq_formated,seq_formated02)
#biexample=biJIAA(seq_formated,seq_formated02)
result=biCompare(biexample)
plot(result)

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