cummeRbund (version 2.14.0)

csSpecificity: 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

"csSpecificity"(object,logMode=T,pseudocount=1,relative=FALSE,...)
"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.

Source

None

Details

None

References

None.

Examples

	data(sampleData)
	csSpecificity(sampleGeneSet)