spliceR (version 1.14.0)

topIsoShift: Returns top transcripts in terms of isoform switching

Description

Returns top transcripts in terms of isoform switching.

Usage

topIsoShift(spliceRObject, n=10)

Arguments

spliceRObject

a SpliceRList object, that has been successfully analyzed and annotated by spliceR.

n

An integer, giving the number of transcripts to return.

Value

A dataframe, containing a cast of the GRanges rows of the highest scoring transcripts by dIF.

Details

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.

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'))

#Get top dIF transcripts
topIsoShift(mySpliceRList, n=20)