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" |