annotateGeneModel {GeneStructureTools}R Documentation

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

Description

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

Usage

annotateGeneModel(transcripts, orfs)

Arguments

transcripts

GRanges of gene model to be visualised

orfs

ORF predictions. Created by getORFs()

Value

data.frame of a gene model for visualisation

Author(s)

Beth Signal

See Also

Other Gviz gene structure visualisation: makeGeneModel

Examples

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)

[Package GeneStructureTools version 1.8.0 Index]