spliceR (version 1.14.0)

totalNumberOfAS: Returns total number of alternative splicing events

Description

Returns total number of alternative splicing events an SpliceRList.

Usage

totalNumberOfAS(spliceRObject)

Arguments

spliceRObject

a SpliceRList object returned by spliceRPlot.

Value

A vector, giving the total number of splicing events for each splice class.

Details

This helper function returns number of total number of alternative splicing events. Object must be analyzed by spliceRPlot first.

References

Vitting-Seerup K , Porse BT, Sandelin A, Waage J. (2014) spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data. BMC Bioinformatics 15:81.

Examples

#Load cufflinks example data
cuffDB <- prepareCuffExample()

#Generate SpliceRList from cufflinks data
cuffDB_spliceR <- prepareCuff(cuffDB)

#Reduce dataset size for fast example runtime
cuffDB_spliceR[[1]] <- cuffDB_spliceR[[1]][1:500]

#Run spliceR
mySpliceRList <- spliceR(cuffDB_spliceR, compareTo='preTranscript', filters=c('expressedGenes','geneOK', 'isoOK', 'expressedIso', 'isoClass'))

#Plot number of exon skipping/inclusion events 
mySpliceRList <- spliceRPlot(mySpliceRList, evaluate="nr_AS", asType="ESI")

totalNumberOfAS(mySpliceRList)