summariseExonTypes: Summarise exon biotypes to broader categories
In GeneStructureTools: Tools for spliced gene structure manipulation and analysis

Description Usage Arguments Value Author(s) See Also Examples

Summarise exon biotypes to broader categories

1	summariseExonTypes(types)

types

vector of exon biotypes

vector of broader exon biotypes

Beth Signal

Other DEXSeq processing methods: DEXSeqIdsToGeneIds, findDEXexonType

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)