spliceR: Splice class detection from assembled RNA-seq data

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

Description

Splice class detection from assembled RNA-seq data.

Usage

spliceR(transcriptData, compareTo, filters, expressionCutoff=0, useProgressBar=T)

Arguments

transcriptData	a SpliceRList object, either created manually from transcript and exon information (see SpliceRList), or created by prepareCuff from CuffLinks data.
compareTo	a character, either 'preTranscript', for comparison to the hypothetical pre-splicing transcript for each gene, or a character, indicating the reference sample against which to classify splicing events.
filters	vector, giving the filters that should be applied - any combinations of 'geneOK', 'expressedGenes', 'sigGenes', 'isoOK', 'expressedIso', 'isoClass' and/or 'sigIso'. Works only for data from Cufflinks, as a manually generated SpliceRList does not include these metacolumns.
expressionCutoff	Numeric, giving the expression threshold (often in FPKM) used for the 'expressedGenes' and 'expressedIso' filter. Default value is 0.
useProgressBar	Boolean, indicating whether to use progressbars. For compatibility. Default = TRUE.

Details

The following filters are allowed for filters: geneOK requires Cufflinks to have reported the quantification of the gene as OK. Only works on transcript data from Cufflinks. expressedGenes requires the parent gene to be expressed. sigGenes requires the parent gene to be expressed in at least one sample. isoOK requires cufflinks to have reported the quantification of the isoform as OK. Only works on transcript data from Cufflinks. expressedIso requires the isoform to be expressed in at least one sample. isoClass removed transcripts marked by cufflinks to be either 'possible pre-mRNA fragment', 'Possible polymerase run-on fragment', or 'Repeat'. Only works on transcript data from Cufflinks. sigIso requires cufflinks to have reported the isoform as significant deregulated between samples. Only works on transcript data from Cufflinks.

Value

A SpliceRList, identical to input SpliceRList transcriptData, with the transcript_features slot containing the following additional columns:

spliceR.major	yes/no, indicating if this isoform is the major isoform expressed of the relevant gene for the reference sample.
spliceR.IF1	Isoform Fraction of total gene expression for sample 1
spliceR.IF2	Isoform Fraction of total gene expression for sample 2
spliceR.dIF	Delta IF (sample 2-sample 1)
spliceR.ESI	Number of exon skipping/inclusion events for this isoform
spliceR.MEE	Number of mutually exclusive exon events for this isoform
spliceR.MESI	Number of mutliple exon skipping/inclusion events for this isoform
spliceR.ISI	Number of intron skipping/retention events for this isoform
spliceR.A5	Number of alternative 5' splice site events for this isoform
spliceR.A3	Number of alternative 3' splice site events for this isoform
spliceR.ATSS	0/1, 1 indicating that this isoform uses an alternative transcription start site
spliceR.ATTS	0/1, 1 indicating that this isoform uses an alternative transcription terminating site
spliceR.analyzed	Yes/no, indicating if this isoform was analyzed(yes), or removed in filtering(no)
spliceR.ESI.start	Genomic start location(s) of ESI elements spliced in/out
spliceR.ESI.end	Genomic end location(s) of ESI elements spliced in/out
spliceR.MEE.start	Genomic start location(s) of MEE elements spliced in/out
spliceR.MEE.end	Genomic end location(s) of MEE elements spliced in/out
spliceR.MESI.end	Genomic end location(s) of MESI elements spliced in/out
spliceR.MESI.start	Genomic start location(s) of MESI elements spliced in/out
spliceR.ISI.start	Genomic start location(s) of ISI elements spliced in/out
spliceR.ISI.end	Genomic end location(s) of ISI elements spliced in/out
spliceR.A5.start	Genomic start location(s) of A5 elements spliced in/out
spliceR.A5.end	Genomic end location(s) of A5 elements spliced in/out
spliceR.A3.start	Genomic start location(s) of A3 elements spliced in/out
spliceR.A3.end	Genomic end location(s) of A3 elements spliced in/out
spliceR.ATSS.start	Genomic start location(s) of ATSS elements spliced in/out
spliceR.ATSS.end	Genomic end location(s) of ATSS elements spliced in/out
spliceR.ATTS.start	Genomic start location(s) of ATTS elements spliced in/out
spliceR.ATTS.end	Genomic end location(s) of ATTS elements spliced in/out

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'))

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