filterGtfOverlap: Filter a GTF overlap to remove exons when exon is annotated...
In GeneStructureTools: Tools for spliced gene structure manipulation and analysis

Description Usage Arguments Value Author(s) See Also Examples

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

1	filterGtfOverlap(gtf.from)

gtf.from

GRanges object of the GTF produced from an overlap

GRanges object of the GTF with redundant exons removed

Beth Signal

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

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])