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.

AuthorZhenpeng Li, Yang Huang, Yabo Ouyang, Yiming Shao, Liying Ma
Date of publicationNone
MaintainerZhenpeng Li<zpli21@gmail.com>
LicenseGPL-2
Version1.16.0

View on Bioconductor

Functions

biCkaksAA Man page
biCkaksAA-class Man page
biCkaksCodon Man page
biCkaksCodon-class Man page
biCompare Man page
biCompare.biCkaksAA Man page
biCompare,biCkaksAA-method Man page
biCompare.biCkaksCodon Man page
biCompare,biCkaksCodon-method Man page
biCompare.biJIAA Man page
biCompare,biJIAA-method Man page
biCompare.biMIAA Man page
biCompare,biMIAA-method Man page
biCompare.biMICodon Man page
biCompare,biMICodon-method Man page
biCompare-class Man page
biCompare-methods Man page
biJIAA Man page
biJIAA-class Man page
biMIAA Man page
biMIAA-class Man page
biMICodon Man page
biMICodon-class Man page
ckaks Man page
ckaksAA Man page
ckaks-class Man page
ckaksCodon Man page
ckaks.CorMut Man page
ckaks.CorMut,ckaks-method Man page
CorMut Man page
CorMut-package Man page
filterSites Man page
filterSites.ckaks Man page
filterSites,ckaks-method Man page
filterSites.JI Man page
filterSites,JI-method Man page
filterSites.kaksAA Man page
filterSites,kaksAA-method Man page
filterSites.kaksCodon Man page
filterSites,kaksCodon-method Man page
filterSites-methods Man page
filterSites.MI Man page
filterSites,MI-method Man page
jiAA Man page
JI-class Man page
ji.CorMut,JI-method Man page
ka.CorMut Man page
ka.CorMut,kaksAA-method Man page
ka.CorMut,kaksCodon-method Man page
kaksAA Man page
kaksAA-class Man page
kaksCodon Man page
kaksCodon-class Man page
kaks.CorMut Man page
kaks.CorMut,kaksAA-method Man page
kaks.CorMut,kaksCodon-method 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
miAA Man page
MI-class Man page
miCodon Man page
mi.CorMut Man page
mi.CorMut,MI-method Man page
plot Man page
plot.biCompare Man page
plot,biCompare-method Man page
plot.ckaks Man page
plot,ckaks-method Man page
plot.JI Man page
plot,JI-method Man page
plot.MI Man page
plot,MI-method Man page
positiveSite01.CorMut Man page
positiveSite01.CorMut,biCompare-method Man page
positiveSite02.CorMut Man page
positiveSite02.CorMut,biCompare-method Man page
p.value.CorMut Man page
p.value.CorMut,JI-method Man page
p.value.CorMut,MI-method Man page
q.CorMut Man page
q.CorMut,kaksAA-method Man page
q.CorMut,kaksCodon-method Man page
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,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,JI-method Man page
show,kaksAA-method Man page
show,kaksCodon-method Man page
show,MI-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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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