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 1.2.1 Index]