totalNumberOfAS: Returns total number of alternative splicing events

In spliceR: Classification of alternative splicing and prediction of coding potential from RNA-seq data.

Description

Returns total number of alternative splicing events an SpliceRList.

Usage

totalNumberOfAS(spliceRObject)

Arguments

spliceRObject

a SpliceRList object returned by spliceRPlot.

Details

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

Value

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

Author(s)

Kristoffer Vitting-Seerup, Johannes Waage

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)

spliceR documentation built on May 2, 2018, 2:50 a.m.