NBSpliceRes-class: NBSpliceRes S4 class implementation in R
In NBSplice: Negative Binomial Models to detect Differential Splicing

Description Slots Features Functions Author(s) See Also Examples

This S4 class represents a data set containing NBTest results results.

results: Data.frame with NBTest results of expressed isoforms.
lowExpIndex: Numeric indicating the positions of low expressed isoforms.
contrast: Character indicating the contrast used for NBTest.
dispersion: Numeric model dispersions.

Explore differential splicing occurrence.
Explore isoform relative expression an its changes.
Combine the results of both gene and isoform levels analysis.

NBSpliceRes S4 class includes the following functions:

initialize: Constructor of NBSpliceRes objects.
results: Gets the results slot.
contrast: Gets the contrast slot.
lowExpIndex: Gets the lowExpIdx slot.
disp: Gets the dispersion slot.
print: Shows a NBSpliceRes object.
show: Shows a NBSpliceRes object.
GetDSGenes: Returns the list of differentially spliced genes.
GetDSResults: Returns the differential splicing results.
GetGeneResults: Returns the NBSplice results for an specific gene.

Gabriela A. Merino merino.gabriela33@gmail.com and Elmer A. Fernandez efernandez@bdmg.com.ar

Other NBSpliceRes: GetDSGenes, GetDSResults, GetGeneResults, NBSpliceRes-initialize, NBSpliceRes, myDSResults, plotGeneResults, plotRatiosDisp, plotVolcano

data(myDSResults, package="NBSplice")
myResults<-results(myDSResults, filter=FALSE)
myLowExpIdx<-lowExpIndex(myDSResults)
myContrast<-contrast(myDSResults)

myNewDSResults<-NBSpliceRes(myResults, myLowExpIdx, myContrast)

##Getting differentially spliced genes
myDSGenes<-GetDSGenes(myDSResults)

##Getting the results for differentially spliced genes
myDSResultsDF<-GetDSResults(myDSResults)

##Getting the results for a particular differentially spliced gene
myResults<-results(myDSResults)

## Select the first gene
gene<-myResults[,"gene"][1]

myGeneResults<-GetGeneResults(myDSResults, gene)