tools: Returns the transcript or exon GRanges from a SpliceRList...

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

Description

Returns the transcript or exon GRanges object from a SpliceRList object.

Usage

transcripts(transcriptData)
exons(transcriptData)

Arguments

transcriptData

a SpliceRList object.

Details

These helper functions returns either the "transcript_features" or "exon_features" object of a SpliceRList object.

Value

A GRanges object. See SpliceRList for a full description of the contents of a SpliceRList.

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)

myTranscripts <- transcripts(cuffDB_spliceR)
myExons <- exons(cuffDB_spliceR)

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