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)

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