csSpecificity {cummeRbund} | R Documentation

## csSpecificity

### Description

Returns a matrix of 'Specificity scores' (S) defined as 1-JSD(p_g,q_i) where p_g is the Log10+1 expression profile of a gene g across all conditions j, collapsed into a probability distribution, and q_i is the unit vector of 'perfect expression' in a given condition i.

### Usage

    ## S4 method for signature 'CuffFeatureSet'
    csSpecificity(object,logMode=T,pseudocount=1,relative=FALSE,...)
    ## S4 method for signature 'CuffData'
    csSpecificity(object,logMode=T,pseudocount=1,relative=FALSE,...)

### Arguments

`object` | An object of class CuffFeatureSet, CuffGeneSet, or CuffData.
`logMode` | A logical argument to log10-transform FPKM values prior to plotting.
`pseudocount` | Value to be added to FPKM for appropriate log transformation and clustering. (Avoids zero-based errors)
`relative` | A logical argument that when TRUE, will scale the S values from 0-1 by dividing by max(S)
`...` | Additional arguments to fpkmMatrix.

### Details

None

### Author(s)

Loyal A. Goff

### Source

None

### References

None.

### Examples

    	data(sampleData)
    	csSpecificity(sampleGeneSet)

[Package cummeRbund version 2.34.0 Index]