overlapTypes: Annotate introns and exonic parts by overlaping exon biotype

In GeneStructureTools: Tools for spliced gene structure manipulation and analysis

Description

Annotate introns and exonic parts by overlaping exon biotype

Usage

overlapTypes(queryCoords, gtf, set = c("from", "to", "overlap"))

Arguments

queryCoords	GRanges object of the query regions
gtf	GRanges object of the GTF annotated with exon biotypes - i.e. exon, CDS, UTR
set	which overlapping set of exon biotypes to return - to, from, and/or overlap

Value

overlaping types in a data.frame

Author(s)

Beth Signal

Examples

gtfFile <- system.file("extdata","example_gtf.gtf",
package = "GeneStructureTools")
DEXSeqGtfFile <- system.file("extdata","gencode.vM14.dexseq.gtf",
package = "GeneStructureTools")

gtf <- rtracklayer::import(gtfFile)
gtf <- UTR2UTR53(gtf)
DEXSeqGtf <- rtracklayer::import(DEXSeqGtfFile)

overlapTypes(DEXSeqGtf[1:10], gtf)

GeneStructureTools documentation built on Nov. 8, 2020, 6:04 p.m.