csSpecificity {cummeRbund} | R Documentation |
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.
## 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,...)
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. |
None
Loyal A. Goff
None
None.
data(sampleData) csSpecificity(sampleGeneSet)