Detect the correlated mutations based on selection pressure


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Documentation for package ‘CorMut’ version 1.18.0

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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.biJIAA 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
biJIAA Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA"
biJIAA-class Class "biCkaksCodon", "biCkaksAA", "biMICodon" and "biMIAA"
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.CorMut Class "ckaks"
ckaks.CorMut-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.JI filterSites methods
filterSites.kaksAA filterSites methods
filterSites.kaksCodon filterSites methods
filterSites.MI filterSites methods
JI-class Class "JI"
ji.CorMut-method Class "JI"
jiAA Compute the Jaccard index among individual amino mutations
ka.CorMut Class "kaksAA"
ka.CorMut-method Class "kaksAA"
ka.CorMut-method Class "kaksCodon"
kaks.CorMut Class "kaksAA"
kaks.CorMut-method Class "kaksAA"
kaks.CorMut-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.CorMut Class "kaksAA"
ks.CorMut-method Class "kaksAA"
ks.CorMut-method Class "kaksCodon"
lod.CorMut Class "ckaks"
lod.CorMut-method Class "ckaks"
lod.CorMut-method Class "kaksAA"
lod.CorMut-method Class "kaksCodon"
method.CorMut Class "biCompare"
method.CorMut-method Class "biCompare"
MI-class Class "MI"
mi.CorMut Class "MI"
mi.CorMut-method Class "MI"
miAA Compute the mutual information among individual amino mutations
miCodon Compute the mutual information among codons
p.value.CorMut Class "MI"
p.value.CorMut-method Class "JI"
p.value.CorMut-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.JI Plot methods for CorMut package
plot.MI Plot methods for CorMut package
positiveSite01.CorMut Class "biCompare"
positiveSite01.CorMut-method Class "biCompare"
positiveSite02.CorMut Class "biCompare"
positiveSite02.CorMut-method Class "biCompare"
q.CorMut Class "kaksAA"
q.CorMut-method Class "kaksAA"
q.CorMut-method Class "kaksCodon"
seqFormat Process the multiple sequence alignment files
seqFormat-methods Process the multiple sequence alignment files
seq_num.CorMut Class "kaksAA"
seq_num.CorMut-method Class "kaksAA"
seq_num.CorMut-method Class "kaksCodon"
show-method Class "JI"
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.CorMut Class "biCompare"
state_1.CorMut-method Class "biCompare"
state_2.CorMut Class "biCompare"
state_2.CorMut-method Class "biCompare"
statistic_1.CorMut Class "biCompare"
statistic_1.CorMut-method Class "biCompare"
statistic_2.CorMut Class "biCompare"
statistic_2.CorMut-method Class "biCompare"