orfDiff {GeneStructureTools} | R Documentation |
Evaluate changes to ORFs caused by alternative splicing
orfDiff(orfsX, orfsY, filterNMD = TRUE, geneSimilarity = TRUE, compareUTR = TRUE, compareBy = "gene", allORFs = NULL)
orfsX |
orf information for 'normal' transcripts. Generated by getOrfs() |
orfsY |
orf information for 'alternative' transcripts. Generated by getOrfs() |
filterNMD |
filter orf information for transcripts not targeted by nmd first? |
geneSimilarity |
compare orf to all orfs in gene? |
compareUTR |
compare UTRs? |
compareBy |
compare by 'transcript' isoforms or by 'gene' groups |
allORFs |
orf information for all transcripts for novel sequence comparisons. Generated by getOrfs() |
data.frame with orf changes
Beth Signal
Other transcript isoform comparisons: attrChangeAltSpliced
,
transcriptChangeSummary
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$type=="exon"] transcripts <- gtf[gtf$type=="transcript"] g <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10 orfsProteinCoding <- getOrfs(exons[exons$gene_name=="Prex2" & exons$transcript_type=="protein_coding"], BSgenome = g) orfsNMD <- getOrfs(exons[exons$gene_name=="Prex2" & exons$transcript_type=="nonsense_mediated_decay"], BSgenome = g) orfDiff(orfsProteinCoding, orfsNMD, filterNMD=FALSE) 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) orfsSkipped <- getOrfs(ExonSkippingTranscripts[ExonSkippingTranscripts$set=="skipped_exon"], BSgenome = g) orfsIncluded <- getOrfs(ExonSkippingTranscripts[ExonSkippingTranscripts$set=="included_exon"], BSgenome = g) orfDiff(orfsSkipped, orfsIncluded, filterNMD=FALSE)