summariseExonTypes {GeneStructureTools} | R Documentation

## Summarise exon biotypes to broader categories

### Description

Summarise exon biotypes to broader categories

### Usage

    summariseExonTypes(types)

### Arguments

`types` | vector of exon biotypes

### Value

vector of broader exon biotypes

### Author(s)

Beth Signal

### See Also

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

### 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")

    types <- findDEXexonType(rownames(DEXSeqResults), DEXSeqGtf, gtf)
    summarisedTypes <- summariseExonTypes(types)
    table(types, summarisedTypes)

[Package GeneStructureTools version 1.2.1 Index]