totalNumberOfAS {spliceR} | R Documentation |
Returns total number of alternative splicing events an SpliceRList.
totalNumberOfAS(spliceRObject)
spliceRObject |
a |
This helper function returns number of total number of alternative splicing events. Object must be analyzed by spliceRPlot
first.
A vector, giving the total number of splicing events for each splice class.
Kristoffer Vitting-Seerup, Johannes Waage
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.
#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)