ckaks-class

show,ckaks-method

ckaks

ckaks.CorMut

lod.CorMut

ckaks.CorMut,ckaks-method

lod.CorMut,ckaks-method

ckaks class for representing the ckaksCodon/ckaksAA results

classes

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.

Zhenpeng Li

CorMut

Detect the correlated mutations based on selection pressure

ckaks-class function

<dl>
    <dt><code>ckaks</code>:</dt><dd>Object of class <code>"matrix"</code>. Conditional kaks among codons or amino mutations</dd> <dt><code>lod</code>:</dt><dd>Object of class <code>"matrix"</code>. LOD confidence score indicates the significance of correlated mutations</dd> </dl> 

Slots

<dl>
    <dt>filterSites</dt><dd><code>signature(object = "ckaks")</code>: Filter positive selection amino mutations for objects of ckaks class.</dd> <dt>plot</dt><dd><code>signature(object = "ckaks")</code>: Plot the influence network among mutations for objects of ckaks class.</dd> </dl> 

ckaks-class: Class "ckaks"

Description

Arguments

Slots

Methods

See Also

Examples