addIntronInTranscript: Add a retained intron to the transcripts it is skipped by

In betsig/GeneStructureTools: Tools for spliced gene structure manipulation and analysis

Description

Add a retained intron to the transcripts it is skipped by

Usage

addIntronInTranscript(
  flankingExons,
  exons,
  whippetDataSet = NULL,
  match = "exact",
  glueExons = TRUE
)

Arguments

flankingExons	data.frame generataed by findIntronContainingTranscripts()
exons	GRanges object made from a GTF with ONLY exon annotations (no gene, transcript, CDS etc.)
whippetDataSet	whippetDataSet generated from readWhippetDataSet()
match	what type of match replacement should be done? exact: exact matches to the intron only retain: keep non-exact intron match coordinates in spliced sets, and retain them in retained sets replace: replace non-exact intron match coordinates with event coordinates in spliced sets, and retain in retained sets
glueExons	Join together exons that are not seperated by introns?

Value

GRanges with transcripts containing retained introns

Author(s)

Beth Signal

See Also

Other whippet splicing isoform creation: alterTranscriptStartEnds(), findExonContainingTranscripts(), findIntronContainingTranscripts(), findJunctionPairs(), replaceJunction(), skipExonInTranscript()

Examples

gtf <- rtracklayer::import(system.file("extdata", "gencode.vM25.small.gtf", package = "GeneStructureTools"))
exons <- gtf[gtf$type == "exon"]
g <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10

whippetFiles <- system.file("extdata", "whippet_small/",
    package = "GeneStructureTools"
)
wds <- readWhippetDataSet(whippetFiles)

wds.intronRetention <- filterWhippetEvents(wds, eventTypes = "RI")
exons.intronRetention <- findIntronContainingTranscripts(input = wds.intronRetention, exons)
IntronRetentionTranscripts <- addIntronInTranscript(exons.intronRetention, exons,
    whippetDataSet = wds.intronRetention
)

exonsFromGRanges <- exons[exons$transcript_id == "ENSMUST00000040372.13" &
    exons$exon_number %in% c(2, 3)]
intronFromGRanges <- exonsFromGRanges[1]
GenomicRanges::start(intronFromGRanges) <-
    GenomicRanges::end(exonsFromGRanges[exonsFromGRanges$exon_number == 2])
GenomicRanges::end(intronFromGRanges) <-
    GenomicRanges::start(exonsFromGRanges[exonsFromGRanges$exon_number == 3])
exons.intronRetention <- findIntronContainingTranscripts(intronFromGRanges, exons)
addIntronInTranscript(exons.intronRetention, exons, match = "retain")

betsig/GeneStructureTools documentation built on March 31, 2021, 4:43 a.m.