leafcutterTranscriptChangeSummary: Compare open reading frames for whippet differentially...

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

Description

Compare open reading frames for whippet differentially spliced events

Usage

leafcutterTranscriptChangeSummary(
  leafcutterEvents,
  exons,
  FDR = NA,
  combineGeneEvents = FALSE,
  BSgenome,
  NMD = FALSE,
  showProgressBar = TRUE,
  junctions = NULL,
  exportGTF = NULL
)

Arguments

leafcutterEvents	data.frame containing information from the per_intron_results.tab file output from leafcutter.
exons	GRanges gtf annotation of exons
FDR	minimum FDR for events. If left as default (NA), will use FDR=0.05. To stop FDR filtering set to 1.
combineGeneEvents	combine clusters occurring in the same gene? Currently not recommended.
BSgenome	BSGenome object containing the genome for the species analysed
NMD	Use NMD predictions? (Note: notNMD must be installed to use this feature)
showProgressBar	show a progress bar of alternative isoform generation?
junctions	junctions GRanges object from readLeafcutterJunctions()
exportGTF	file name to export alternative isoform GTFs (default=NULL)

Value

data.frame containing significant whippet diff data and ORF change summaries

Author(s)

Beth Signal

Examples

leafcutterFiles <- list.files(system.file("extdata", "leaf_small/", package = "GeneStructureTools"), full.names = TRUE)
leafcutterIntrons <- read.delim(leafcutterFiles[grep("intron_results", leafcutterFiles)], stringsAsFactors = FALSE)
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
leafcutterTranscriptChangeSummary(leafcutterEvents = leafcutterIntrons, exons = exons, BSgenome = g, NMD = FALSE)

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