removeDuplicateTranscripts: Remove transcript duplicates

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

Description

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

Usage

removeDuplicateTranscripts(transcripts)

Arguments

transcripts

GRanges object with transcript structures in exon form

Value

GRanges object with unique transcript structures in exon form

Author(s)

Beth Signal

See Also

Other gtf manipulation: UTR2UTR53(), exonsToTranscripts(), removeSameExon(), reorderExonNumbers()

Examples

gtf <- rtracklayer::import(system.file("extdata", "gencode.vM25.small.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)

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