orfDiff: Evaluate changes to ORFs caused by alternative splicing

In GeneStructureTools: Tools for spliced gene structure manipulation and analysis

Description

Evaluate changes to ORFs caused by alternative splicing

Usage

orfDiff(orfsX, orfsY, filterNMD = TRUE, geneSimilarity = TRUE,
  compareUTR = TRUE, compareBy = "gene", allORFs = NULL)

Arguments

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()

Value

data.frame with orf changes

Author(s)

Beth Signal

See Also

Other transcript isoform comparisons: attrChangeAltSpliced, transcriptChangeSummary

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$type=="exon"]
transcripts <- gtf[gtf$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)

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