Compute the mutual information among codons

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Description

Compute the mutual information among codons, the amino mutation in a site will be treated as whole in computation.

Usage

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miCodon(seq_formated, kaks = TRUE, lod_cut = 2, setPosition = c(),fdr=FALSE)

Arguments

seq_formated

Formated alignment sequence. i.e. the result after the treatment of DataFormatCorMut.

kaks

A logical variable to indicate whether kaks is turn on or off, if kaks is TRUE, conditional kaks will be computed only among positive seelction sites, or if kaks is FALSE, conditional kaks will be computed only among all sites of sequence.

lod_cut

The LOD confidence score cutoff, the default value is 2. If lod is larger than 2, it means the positive selection of individual site or the conditional selection pressure among sites are significant.

setPosition

The positions of sequence to compute. setPosition should be a vector of interger type.

fdr

Decide whether use FDR procedure to control the p value of the computation.The default value is False.

Value

A object of MI class will be return. miCodon includes two slots of matrix:mi and p.value, which indicate the mutual information and p value respectively.

Author(s)

Zhenpeng Li

References

Cover, T. M., Thomas, J. A. & Wiley, J. Elements of information theory. 6, (Wiley Online Library: 1991).

See Also

filterSites,miAA

Examples

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