topIsoShift {spliceR} | R Documentation |
Returns top transcripts in terms of isoform switching.
topIsoShift(spliceRObject, n=10)
spliceRObject |
a |
n |
An integer, giving the number of transcripts to return. |
This helper function returns the transcripts with the highest delta-isoform fraction (dIF) between samples. If the data is based on cufflinks (source_id=="cufflinks"), only isoforms flagged significantly changing between samples will be returned.
A dataframe, containing a cast of the GRanges rows of the highest scoring transcripts by dIF.
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')) #Get top dIF transcripts topIsoShift(mySpliceRList, n=20)