csSpecificity: csSpecificity

In gofflab/cummeRbund-BioC-Bridge: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.

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)

gofflab/cummeRbund-BioC-Bridge documentation built on May 17, 2019, 7:30 a.m.