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

In GeneStructureTools: Tools for spliced gene structure manipulation and analysis

Description

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

Usage

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

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.