attrChangeAltSpliced {GeneStructureTools} | R Documentation |
Evaluate the change in an attribute between a set of 'normal' transcripts and 'alternative' transcripts
attrChangeAltSpliced(orfsX, orfsY, attribute = "orf_length", compareBy = "gene", useMax = TRUE, compareUTR = FALSE)
orfsX |
orf information for 'normal' transcripts. Generated by getOrfs() |
orfsY |
orf information for 'alternative' transcripts. Generated by getOrfs() |
attribute |
attribute to compare |
compareBy |
compare by 'transcript' isoforms or by 'gene' groups |
useMax |
use max as the summary function when multiple isoforms are aggregated? If FALSE, will use min instead. |
compareUTR |
compare the UTR lengths between transcripts? Only runs if attribute = "orf_length" |
data.frame with attribute changes
Beth Signal
Other transcript isoform comparisons: orfDiff
,
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 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) attrChangeAltSpliced(orfsSkipped, orfsIncluded,attribute = "orf_length")