findExonContainingTranscripts: Given the location of a whole spliced in exon, find...

Description Usage Arguments Value Author(s) See Also Examples

View source: R/ExonSkipping.R

Description

Given the location of a whole spliced in exon, find transcripts which can splice out this exon

Usage

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findExonContainingTranscripts(input, exons, variableWidth = 0,
  findIntrons = FALSE, transcripts)

Arguments

input

whippetDataSet generated from readWhippetDataSet() or a Granges of exon coordinates

exons

GRanges object made from a GTF containing exon coordinates

variableWidth

How many nts overhang is allowed for finding matching exons (default = 0, i.e. complete match)

findIntrons

Find transcripts where the event occurs within the intron?

transcripts

GRanges object made from a GTF containing transcript coordinates (only required if findIntrons=TRUE)

Value

data.frame with all overlapping exons

Author(s)

Beth Signal

See Also

Other whippet splicing isoform creation: addIntronInTranscript, findIntronContainingTranscripts, findJunctionPairs, replaceJunction, skipExonInTranscript

Examples

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

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

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

exonFromGRanges <- exons[exons$exon_id == "ENSMUSE00001271768.1"]
exons.exonSkip <- findExonContainingTranscripts(exonFromGRanges, exons,
variableWidth=0, findIntrons=FALSE, transcripts)

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