transcriptChangeSummary {GeneStructureTools} | R Documentation |
Compare open reading frames for two sets of paired transcripts
transcriptChangeSummary(transcriptsX, transcriptsY, BSgenome, exons, NMD = FALSE, NMDModel = NULL, compareBy = "gene", orfPrediction = "allFrames", compareToGene = FALSE, whippetDataSet = NULL, exportGTF = NULL)
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= |
compareToGene |
compare alternative isoforms to all normal gene isoforms (in exons) |
whippetDataSet |
whippetDataSet generated from |
exportGTF |
file name to export alternative isoform GTFs (default= |
Summarised ORF changes data.frame
Beth Signal
Other transcript isoform comparisons: attrChangeAltSpliced
,
orfDiff
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)