overlapTypes {GeneStructureTools} | R Documentation

## Annotate introns and exonic parts by overlaping exon biotype

### 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)

[Package GeneStructureTools version 1.2.1 Index]