findDEXexonType {GeneStructureTools} | R Documentation |
Find a DEXSeq exons' biotype
findDEXexonType(DEXSeqExonId, DEXSeqGtf, gtf, set = "overlap")
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 |
overlaping types
Beth Signal
Other DEXSeq processing methods: DEXSeqIdsToGeneIds
,
summariseExonTypes
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)