findDEXexonType: Find a DEXSeq exons' biotype

In GeneStructureTools: Tools for spliced gene structure manipulation and analysis

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)

GeneStructureTools documentation built on Nov. 8, 2020, 6:04 p.m.