annotateGeneModel: Annotate a GRanges gene model with ORF boundries for...
In GeneStructureTools: Tools for spliced gene structure manipulation and analysis

Description Usage Arguments Value Author(s) See Also Examples

Annotate a GRanges gene model with ORF boundries for visualisation with Gviz

1	annotateGeneModel(transcripts, orfs)

`transcripts`	GRanges of gene model to be visualised
`orfs`	ORF predictions. Created by getORFs()

data.frame of a gene model for visualisation

Beth Signal

Other Gviz gene structure visualisation: makeGeneModel

gtf <- rtracklayer::import(system.file("extdata", "example_gtf.gtf",
package="GeneStructureTools"))
transcript <- gtf[gtf$type=="exon" & gtf$gene_name=="Neurl1a"]
g <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10
# longest ORF for each transcripts
orfs <- getOrfs(transcript, BSgenome = g, returnLongestOnly = TRUE)
geneModelAnnotated <- annotateGeneModel(transcript, orfs)