removeDuplicateTranscripts: Remove transcript duplicates
In GeneStructureTools: Tools for spliced gene structure manipulation and analysis

Description Usage Arguments Value Author(s) See Also Examples

View source: R/AltSplicingJunctionSupported.R

Removes Structural duplicates of transcripts in a GRanges object Note that duplicates must have different transcript ids.

1	removeDuplicateTranscripts(transcripts)

transcripts

GRanges object with transcript structures in exon form

GRanges object with unique transcript structures in exon form

Beth Signal

Other gtf manipulation: UTR2UTR53, addBroadTypes, exonsToTranscripts, filterGtfOverlap, removeSameExon, reorderExonNumbers

gtf <- rtracklayer::import(system.file("extdata","example_gtf.gtf",
package = "GeneStructureTools"))
exons <- gtf[gtf$type=="exon"]
exons.altName <- exons
exons.altName$transcript_id <- paste(exons.altName$transcript_id, "duplicated", sep="_")
exons.duplicated <- c(exons, exons.altName)
length(exons.duplicated)
exons.deduplicated <- removeDuplicateTranscripts(exons.duplicated)
length(exons.deduplicated)