CorMut: Detect the correlated mutations based on selection pressure

CorMut provides functions for computing kaks for individual sites or specific amino acids and detecting correlated mutations among them. Three methods are provided for detecting correlated mutations ,including conditional selection pressure, mutual information and Jaccard index. The computation consists of two steps: First, the positive selection sites are detected; Second, the mutation correlations are computed among the positive selection sites. Note that the first step is optional. Meanwhile, CorMut facilitates the comparison of the correlated mutations between two conditions by the means of correlated mutation network.

Author
Zhenpeng Li, Yang Huang, Yabo Ouyang, Yiming Shao, Liying Ma
Date of publication
None
Maintainer
Zhenpeng Li<zpli21@gmail.com>
License
GPL-2
Version
1.16.0

View on Bioconductor

Man pages

biCkaksCodon-class
Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA"
biCompare-class
Class "biCompare"
biCompare-methods
biCompare implement biCompare methods for comparison of the...
ckaksAA
Compute the conditional kaks(conditional selection pressure)...
ckaks-class
Class "ckaks"
ckaksCodon
Compute the conditional kaks(conditional selection pressure)...
CorMut-package
Detect the correlated mutations based on selection pressure
filterSites-methods
filterSites methods
jiAA
Compute the Jaccard index among individual amino mutations
JI-class
Class "JI"
kaksAA
Compute kaks for individual amino mutation
kaksAA-class
Class "kaksAA"
kaksCodon
Compute kaks for individual codon
kaksCodon-class
Class "kaksCodon"
miAA
Compute the mutual information among individual amino...
MI-class
Class "MI"
miCodon
Compute the mutual information among codons
plot-methods
Plot methods for CorMut package
seqFormat-methods
Process the multiple sequence alignment files

Files in this package

CorMut/DESCRIPTION
CorMut/NAMESPACE
CorMut/R
CorMut/R/ClassMethod.R
CorMut/R/CorMut-internal.R
CorMut/R/S4accessor.R
CorMut/R/biCompare_method.R
CorMut/R/ckaksAA.R
CorMut/R/ckaks_codon.R
CorMut/R/freqCompute.R
CorMut/R/jiAA.R
CorMut/R/kaksAA.R
CorMut/R/kaksCodon.R
CorMut/R/miAA.R
CorMut/R/miCodon.R
CorMut/R/seqFormat.R
CorMut/build
CorMut/build/vignette.rds
CorMut/inst
CorMut/inst/doc
CorMut/inst/doc/CorMut.R
CorMut/inst/doc/CorMut.Rnw
CorMut/inst/doc/CorMut.pdf
CorMut/inst/extdata
CorMut/inst/extdata/PI_treatment.aln
CorMut/inst/extdata/PI_treatment_naive.aln
CorMut/man
CorMut/man/CorMut-package.Rd
CorMut/man/JI-class.Rd
CorMut/man/MI-class.Rd
CorMut/man/biCkaksCodon-class.Rd
CorMut/man/biCompare-class.Rd
CorMut/man/biCompare-methods.Rd
CorMut/man/ckaks-class.Rd
CorMut/man/ckaksAA.Rd
CorMut/man/ckaksCodon.Rd
CorMut/man/filterSites-methods.Rd
CorMut/man/jiAA.Rd
CorMut/man/kaksAA-class.Rd
CorMut/man/kaksAA.Rd
CorMut/man/kaksCodon-class.Rd
CorMut/man/kaksCodon.Rd
CorMut/man/miAA.Rd
CorMut/man/miCodon.Rd
CorMut/man/plot-methods.Rd
CorMut/man/seqFormat-methods.Rd
CorMut/vignettes
CorMut/vignettes/CorMut.Rnw