transcriptChangeSummary: Compare open reading frames for two sets of paired...

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

Description

Compare open reading frames for two sets of paired transcripts

Usage

transcriptChangeSummary(
  transcriptsX,
  transcriptsY,
  BSgenome,
  exons,
  dataSet = NULL,
  exportGTF = NULL,
  NMD = FALSE,
  compareBy = "gene",
  orfPrediction = "allFrames",
  compareToGene = FALSE,
  selectLongest = 1
)

Arguments

transcriptsX	GRanges object with exon annotations for all transcripts to be compared for the 'normal' condition
transcriptsY	GRanges object with exon annotations for all transcripts to be compared for the 'alternative' condition
BSgenome	BSGenome object containing the genome for the species analysed
exons	GRanges object made from a GTF containing exon coordinates
dataSet	whippetDataSet/rMATSDataSet generated from readWhippetDataSet() or readrMATSDataSet() Use if PSI directionality should be taken into account when comparing isoforms.
exportGTF	file name to export alternative isoform GTFs (default=NULL)
NMD	Use NMD predictions? This will filter ORFs out of comparisons if they are likely to be NMD-targeted.
compareBy	compare isoforms by 'transcript' id, or aggregate all changes occurring by 'gene'
orfPrediction	What type of orf predictions to return. default= "allFrames"
compareToGene	compare alternative isoforms to all normal gene isoforms (in exons)
selectLongest	passed to getORFs()

Value

Summarised ORF changes data.frame

Author(s)

Beth Signal

See Also

Other transcript isoform comparisons: attrChangeAltSpliced(), orfDiff()

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)
transcriptChangeSummary(ExonSkippingTranscripts[ExonSkippingTranscripts$set == "included_exon"],
    ExonSkippingTranscripts[ExonSkippingTranscripts$set == "skipped_exon"],
    BSgenome = g, exons
)

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