filterGtfOverlap {GeneStructureTools}R Documentation

Filter a GTF overlap to remove exons when exon is annotated as a CDS/UTR

Description

Filter a GTF overlap to remove exons when exon is annotated as a CDS/UTR

Usage

filterGtfOverlap(gtf.from)

Arguments

gtf.from

GRanges object of the GTF produced from an overlap

Value

GRanges object of the GTF with redundant exons removed

Author(s)

Beth Signal

See Also

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

Examples

gtfFile <- system.file("extdata","example_gtf.gtf",
package = "GeneStructureTools")
gtf <- rtracklayer::import(gtfFile)
overlap <- as.data.frame(GenomicRanges::findOverlaps(gtf[which(gtf$type=="CDS")[1]], gtf))
table(gtf$type[overlap$subjectHits])
overlapFiltered <- filterGtfOverlap(gtf[overlap$subjectHits])
table(overlapFiltered$type[overlap$subjectHits])
overlap <- as.data.frame(GenomicRanges::findOverlaps(gtf[which(
gtf$transcript_type=="retained_intron")[1]],gtf))
table(gtf$type[overlap$subjectHits])
overlapFiltered <- filterGtfOverlap(gtf[overlap$subjectHits])
table(overlapFiltered$type[overlap$subjectHits])

[Package GeneStructureTools version 1.12.0 Index]