annotateGeneModel: Annotate a GRanges gene model with ORF boundries for...

In betsig/GeneStructureTools: Tools for spliced gene structure manipulation and analysis

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", "gencode.vM25.small.gtf",
    package = "GeneStructureTools"
))
transcript <- gtf[gtf$type == "exon" & gtf$gene_name == "Tmem208"]
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)

betsig/GeneStructureTools documentation built on March 31, 2021, 4:43 a.m.