alterTranscriptStartEnds: Find transcripts overlapping first/last exons and alter their...

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

Description

Find transcripts overlapping first/last exons and alter their transcription start site or transcription end site

Usage

alterTranscriptStartEnds(whippetDataSet, exons, unfilteredWDS, type = NA)

Arguments

whippetDataSet	whippetDataSet generated from readWhippetDataSet()
exons	GRanges object made from a GTF containing exon coordinates
unfilteredWDS	unfiltered whippetDataSet generated from readWhippetDataSet() Note that this should contain ALL TS/TE events, regardless of significance, as these are used to contruct the entire exon range.
type	type of Whippet event (TS/TE). Note only one event type should be processed at a time.

Value

GRanges object with transcripts containing alternative junctions.

Author(s)

Beth Signal

See Also

Other whippet splicing isoform creation: addIntronInTranscript(), 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.TS <- filterWhippetEvents(wds, eventTypes = "TS", psiDelta = 0.1, probability = 0.95)
alterTranscriptStartEnds(whippetDataSet = wds.TS, exons = exons, unfilteredWDS = wds, type = "TS")

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