NBSpliceRes-class: NBSpliceRes S4 class implementation in R

Description Slots Features Functions Author(s) See Also Examples

Description

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

Slots

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.

Features

  1. Explore differential splicing occurrence.

  2. Explore isoform relative expression an its changes.

  3. Combine the results of both gene and isoform levels analysis.

Functions

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.

Author(s)

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

See Also

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

Examples

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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)

NBSplice documentation built on Nov. 8, 2020, 8:07 p.m.