orfDiff: Evaluate changes to ORFs caused by alternative splicing

In betsig/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,
  uniprotData = NULL,
  uniprotSeqFeatures = 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()
uniprotData	data.frame of uniprot sequence information
uniprotSeqFeatures	data.frame of uniprot sequecne features

Value

data.frame with orf changes

Author(s)

Beth Signal

See Also

Other transcript isoform comparisons: attrChangeAltSpliced(), transcriptChangeSummary()

Examples

gtf <- rtracklayer::import(system.file("extdata", "gencode.vM25.small.gtf", package = "GeneStructureTools"))
exons <- gtf[gtf$type == "exon"]
g <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10

whippetFiles <- system.file("extdata", "whippet_small/",
    package = "GeneStructureTools"
)
wds <- readWhippetDataSet(whippetFiles)

wds.exonSkip <- filterWhippetEvents(wds, eventTypes = "CE", psiDelta = 0.2)
exons.exonSkip <- findExonContainingTranscripts(wds.exonSkip, exons,
    variableWidth = 0, findIntrons = FALSE
)
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)

orfsProteinCoding <- getOrfs(exons[exons$gene_name == "Tmem208" &
    exons$transcript_type == "protein_coding"], BSgenome = g)
orfsNMD <- getOrfs(exons[exons$gene_name == "Tmem208" &
    exons$transcript_type == "nonsense_mediated_decay"], BSgenome = g)
orfDiff(orfsProteinCoding, orfsNMD, filterNMD = FALSE)

betsig/GeneStructureTools documentation built on March 31, 2021, 4:43 a.m.