filterGtfOverlap {GeneStructureTools} | R Documentation |
Filter a GTF overlap to remove exons when exon is annotated as a CDS/UTR
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])