findDEXexonType {GeneStructureTools} | R Documentation

## Find a DEXSeq exons' biotype

### Description

Find a DEXSeq exons' biotype

### Usage

    findDEXexonType(DEXSeqExonId, DEXSeqGtf, gtf, set = "overlap")

### Arguments

`DEXSeqExonId` | vector of DEXSeq exon ids
`DEXSeqGtf` | GRanges object of the DEXSeq formatted gtf
`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

### Author(s)

Beth Signal

### See Also

Other DEXSeq processing methods: `DEXSeqIdsToGeneIds`, `summariseExonTypes`

### 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)

    findDEXexonType("ENSMUSG00000032366.15:E028", DEXSeqGtf, gtf)

    DEXSeqResultsFile <- system.file("extdata","dexseq_results_significant.txt",
    package = "GeneStructureTools")
    DEXSeqResults <- read.table(DEXSeqResultsFile, sep="\t")

    findDEXexonType(rownames(DEXSeqResults), DEXSeqGtf, gtf)

[Package GeneStructureTools version 1.2.1 Index]