skipExonInTranscript: Remove and include a skipped exon from the transcripts it...

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

Description

Remove and include a skipped exon from the transcripts it overlaps

Usage

skipExonInTranscript(
  skippedExons,
  exons,
  glueExons = TRUE,
  whippetDataSet = NULL,
  match = "exact"
)

Arguments

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

Value

GRanges with transcripts skipping exons

Author(s)

Beth Signal

See Also

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

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.exonSkip <- filterWhippetEvents(wds, eventTypes = "CE", psiDelta = 0.2)
exons.exonSkip <- findExonContainingTranscripts(wds.exonSkip, exons,
    variableWidth = 0, findIntrons = FALSE
)
ExonSkippingTranscripts <- skipExonInTranscript(exons.exonSkip, exons, whippetDataSet = wds.exonSkip)

exonFromGRanges <- exons[exons$exon_id == "ENSMUSE00000414559.2"]
exons.exonSkip <- findExonContainingTranscripts(exonFromGRanges, exons,
    variableWidth = 0, findIntrons = FALSE
)
ExonSkippingTranscripts <- skipExonInTranscript(exons.exonSkip, exons, match = "skip")

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