CorMut: Detect the correlated mutations based on selection pressure
Version 1.18.0

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.

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AuthorZhenpeng Li, Yang Huang, Yabo Ouyang, Yiming Shao, Liying Ma
Bioconductor views Sequencing
Date of publicationNone
MaintainerZhenpeng Li<zpli21@gmail.com>
LicenseGPL-2
Version1.18.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CorMut")

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

Functions

CorMut Man page
CorMut-package Man page
JI-class Man page
MI-class Man page
Ntnv Source code
Ntnv_aa Source code
biCkaksAA Man page Source code
biCkaksAA-class Man page
biCkaksCodon Man page Source code
biCkaksCodon-class Man page
biCompare Man page
biCompare,biCkaksAA-method Man page
biCompare,biCkaksCodon-method Man page
biCompare,biJIAA-method Man page
biCompare,biMIAA-method Man page
biCompare,biMICodon-method Man page
biCompare-class Man page
biCompare-methods Man page
biCompare.biCkaksAA Man page
biCompare.biCkaksCodon Man page
biCompare.biJIAA Man page
biCompare.biMIAA Man page
biCompare.biMICodon Man page
biJIAA Man page Source code
biJIAA-class Man page
biMIAA Man page Source code
biMIAA-class Man page
biMICodon Man page Source code
biMICodon-class Man page
ckaks Man page
ckaks-class Man page
ckaks.CorMut Man page
ckaks.CorMut,ckaks-method Man page
ckaksAA Man page Source code
ckaksCodon Man page Source code
filterSites Man page
filterSites,JI-method Man page
filterSites,MI-method Man page
filterSites,ckaks-method Man page
filterSites,kaksAA-method Man page
filterSites,kaksCodon-method Man page
filterSites-methods Man page
filterSites.JI Man page
filterSites.MI Man page
filterSites.ckaks Man page
filterSites.kaksAA Man page
filterSites.kaksCodon Man page
freqCompute Source code
fvft Source code
genericSlot Source code
ji.CorMut,JI-method Man page
jiAA Man page Source code
ka.CorMut Man page
ka.CorMut,kaksAA-method Man page
ka.CorMut,kaksCodon-method Man page
kaks.CorMut Man page
kaks.CorMut,kaksAA-method Man page
kaks.CorMut,kaksCodon-method Man page
kaksAA Man page Source code
kaksAA-class Man page
kaksCodon Man page Source code
kaksCodon-class Man page
ks.CorMut Man page
ks.CorMut,kaksAA-method Man page
ks.CorMut,kaksCodon-method Man page
lod.CorMut Man page
lod.CorMut,ckaks-method Man page
lod.CorMut,kaksAA-method Man page
lod.CorMut,kaksCodon-method Man page
method.CorMut Man page
method.CorMut,biCompare-method Man page
mi.CorMut Man page
mi.CorMut,MI-method Man page
miAA Man page Source code
miCodon Man page Source code
p.value.CorMut Man page
p.value.CorMut,JI-method Man page
p.value.CorMut,MI-method Man page
plot Man page
plot,JI-method Man page
plot,MI-method Man page
plot,biCompare-method Man page
plot,ckaks-method Man page
plot.JI Man page
plot.MI Man page
plot.biCompare Man page
plot.ckaks Man page
positiveSite01.CorMut Man page
positiveSite01.CorMut,biCompare-method Man page
positiveSite02.CorMut Man page
positiveSite02.CorMut,biCompare-method Man page
q.CorMut Man page
q.CorMut,kaksAA-method Man page
q.CorMut,kaksCodon-method Man page
rawreplace Source code
seqFormat Man page
seqFormat-methods Man page
seq_num.CorMut Man page
seq_num.CorMut,kaksAA-method Man page
seq_num.CorMut,kaksCodon-method Man page
show,JI-method Man page
show,MI-method Man page
show,biCkaksAA-method Man page
show,biCkaksCodon-method Man page
show,biMIAA-method Man page
show,biMICodon-method Man page
show,ckaks-method Man page
show,kaksAA-method Man page
show,kaksCodon-method Man page
state_1.CorMut Man page
state_1.CorMut,biCompare-method Man page
state_2.CorMut Man page
state_2.CorMut,biCompare-method Man page
statistic_1.CorMut Man page
statistic_1.CorMut,biCompare-method Man page
statistic_2.CorMut Man page
statistic_2.CorMut,biCompare-method Man page
weightnorm Source code

Files

DESCRIPTION
NAMESPACE
R
R/ClassMethod.R
R/CorMut-internal.R
R/S4accessor.R
R/biCompare_method.R
R/ckaksAA.R
R/ckaks_codon.R
R/freqCompute.R
R/jiAA.R
R/kaksAA.R
R/kaksCodon.R
R/miAA.R
R/miCodon.R
R/seqFormat.R
build
build/vignette.rds
inst
inst/doc
inst/doc/CorMut.R
inst/doc/CorMut.Rnw
inst/doc/CorMut.pdf
inst/extdata
inst/extdata/PI_treatment.aln
inst/extdata/PI_treatment_naive.aln
man
man/CorMut-package.Rd
man/JI-class.Rd
man/MI-class.Rd
man/biCkaksCodon-class.Rd
man/biCompare-class.Rd
man/biCompare-methods.Rd
man/ckaks-class.Rd
man/ckaksAA.Rd
man/ckaksCodon.Rd
man/filterSites-methods.Rd
man/jiAA.Rd
man/kaksAA-class.Rd
man/kaksAA.Rd
man/kaksCodon-class.Rd
man/kaksCodon.Rd
man/miAA.Rd
man/miCodon.Rd
man/plot-methods.Rd
man/seqFormat-methods.Rd
vignettes
vignettes/CorMut.Rnw
CorMut documentation built on May 20, 2017, 9:19 p.m.