annotateGeneModel {GeneStructureTools} | R Documentation |
Annotate a GRanges gene model with ORF boundries for visualisation with Gviz
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)