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

In betsig/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
)

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? (only required if findIntrons=TRUE)

Value

data.frame with all overlapping exons

Author(s)

Beth Signal

See Also

Other whippet splicing isoform creation: addIntronInTranscript(), alterTranscriptStartEnds(), 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.exonSkip <- filterWhippetEvents(wds, eventTypes = "CE", psiDelta = 0.2)
exons.exonSkip <- findExonContainingTranscripts(wds.exonSkip, exons,
    variableWidth = 0, findIntrons = FALSE
)

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

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