attrChangeAltSpliced: Evaluate the change in an attribute between a set of 'normal'...

In betsig/GeneStructureTools: Tools for spliced gene structure manipulation and analysis

Description

Evaluate the change in an attribute between a set of 'normal' transcripts and 'alternative' transcripts

Usage

attrChangeAltSpliced(
  orfsX,
  orfsY,
  attribute = "orf_length",
  compareBy = "gene",
  useMax = TRUE,
  compareUTR = FALSE
)

Arguments

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"

Value

data.frame with attribute changes

Author(s)

Beth Signal

See Also

Other transcript isoform comparisons: orfDiff(), 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
)
attrChangeAltSpliced(orfsSkipped, orfsIncluded, attribute = "orf_length")

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