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

In 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,
  NMD = FALSE, NMDModel = NULL, compareBy = "gene",
  orfPrediction = "allFrames", compareToGene = FALSE,
  whippetDataSet = NULL, exportGTF = NULL)

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
NMD	Use NMD predictions? (Note: notNMD must be installed to use this feature)
NMDModel	Use the "base" or "lncRNA" NMD model?
compareBy	compare isoforms by 'transcript' id, or aggregate all changes occuring by 'gene'
orfPrediction	What type of orf predictions to return. default= "allFrames"
compareToGene	compare alternative isoforms to all normal gene isoforms (in exons)
whippetDataSet	whippetDataSet generated from readWhippetDataSet() Use if PSI directionality should be taken into account when comparing isoforms.
exportGTF	file name to export alternative isoform GTFs (default=NULL)

Value

Summarised ORF changes data.frame

Author(s)

Beth Signal

See Also

Other transcript isoform comparisons: attrChangeAltSpliced, orfDiff

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"]
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)
ExonSkippingTranscripts <- skipExonInTranscript(exons.exonSkip, exons, whippetDataSet=wds.exonSkip)
transcriptChangeSummary(ExonSkippingTranscripts[ExonSkippingTranscripts$set=="included_exon"],
ExonSkippingTranscripts[ExonSkippingTranscripts$set=="skipped_exon"],
BSgenome=g,exons)

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