Detect the correlated mutations based on selection pressure


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Documentation for package ‘CorMut’ version 1.0.0

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CorMut-package Detect the correlated mutations based on selection pressure
biCkaksAA Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA"
biCkaksAA-class Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA"
biCkaksCodon Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA"
biCkaksCodon-class Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA"
biCompare biCompare implement biCompare methods for comparison of the correlated mutations between two conditions by the means of correlated mutation network
biCompare-class Class "biCompare"
biCompare-method biCompare implement biCompare methods for comparison of the correlated mutations between two conditions by the means of correlated mutation network
biCompare-methods biCompare implement biCompare methods for comparison of the correlated mutations between two conditions by the means of correlated mutation network
biCompare.biCkaksAA biCompare implement biCompare methods for comparison of the correlated mutations between two conditions by the means of correlated mutation network
biCompare.biCkaksCodon biCompare implement biCompare methods for comparison of the correlated mutations between two conditions by the means of correlated mutation network
biCompare.biMIAA biCompare implement biCompare methods for comparison of the correlated mutations between two conditions by the means of correlated mutation network
biCompare.biMICodon biCompare implement biCompare methods for comparison of the correlated mutations between two conditions by the means of correlated mutation network
biMIAA Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA"
biMIAA-class Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA"
biMICodon Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA"
biMICodon-class Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA"
ckaks Class "ckaks"
ckaks-class Class "ckaks"
ckaks-method Class "ckaks"
ckaksAA Compute the conditional kaks(conditional selection pressure) among amino mutations
ckaksCodon Compute the conditional kaks(conditional selection pressure) among codons
CorMut Detect the correlated mutations based on selection pressure
filterSites filterSites methods
filterSites-method filterSites methods
filterSites-methods filterSites methods
filterSites.ckaks filterSites methods
filterSites.kaksAA filterSites methods
filterSites.kaksCodon filterSites methods
filterSites.MI filterSites methods
ka Class "kaksCodon"
ka-method Class "kaksAA"
ka-method Class "kaksCodon"
kaks Class "kaksCodon"
kaks-method Class "kaksAA"
kaks-method Class "kaksCodon"
kaksAA Compute kaks for individual amino mutation
kaksAA-class Class "kaksAA"
kaksCodon Compute kaks for individual codon
kaksCodon-class Class "kaksCodon"
ks Class "kaksCodon"
ks-method Class "kaksAA"
ks-method Class "kaksCodon"
lod Class "kaksCodon"
lod-method Class "ckaks"
lod-method Class "kaksAA"
lod-method Class "kaksCodon"
method Class "biCompare"
method-method Class "biCompare"
mi Class "MI"
MI-class Class "MI"
mi-method Class "MI"
miAA Compute the mutual information among individual amino mutations
miCodon Compute the mutual information among codons
p.value Class "MI"
p.value-method Class "MI"
plot Plot methods for CorMut package
plot-method Plot methods for CorMut package
plot.biCompare Plot methods for CorMut package
plot.ckaks Plot methods for CorMut package
plot.MI Plot methods for CorMut package
positiveSite01 Class "biCompare"
positiveSite01-method Class "biCompare"
positiveSite02 Class "biCompare"
positiveSite02-method Class "biCompare"
q Class "kaksCodon"
q-method Class "kaksAA"
q-method Class "kaksCodon"
seqFormat Process the multiple sequence alignment files
seqFormat-methods Process the multiple sequence alignment files
seq_num Class "kaksCodon"
seq_num-method Class "kaksAA"
seq_num-method Class "kaksCodon"
show-method Class "MI"
show-method Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA"
show-method Class "ckaks"
show-method Class "kaksAA"
show-method Class "kaksCodon"
state_1 Class "biCompare"
state_1-method Class "biCompare"
state_2 Class "biCompare"
state_2-method Class "biCompare"
statistic_1 Class "biCompare"
statistic_1-method Class "biCompare"
statistic_2 Class "biCompare"
statistic_2-method Class "biCompare"