attrChangeAltSpliced {GeneStructureTools}R Documentation

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

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

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")

[Package GeneStructureTools version 1.0.0 Index]