leafcutterTranscriptChangeSummary {GeneStructureTools} | R Documentation |
Compare open reading frames for whippet differentially spliced events
leafcutterTranscriptChangeSummary(significantEvents, combineGeneEvents = FALSE, exons, BSgenome, NMD = FALSE, showProgressBar = TRUE, exportGTF = NULL)
significantEvents |
data.frame containing information from the per_intron_results.tab file output from leafcutter. |
combineGeneEvents |
combine clusters occuring in the same gene? Currently not reccomended. |
exons |
GRanges gtf annotation of exons |
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? |
exportGTF |
file name to export alternative isoform GTFs (default=NULL) |
data.frame containing signficant whippet diff data and ORF change summaries
Beth Signal
leafcutterFiles <- list.files(system.file("extdata","leafcutter/", package = "GeneStructureTools"), full.names = TRUE) leafcutterIntrons <- read.delim(leafcutterFiles[ grep("intron_results", leafcutterFiles)],stringsAsFactors=FALSE) gtf <- rtracklayer::import(system.file("extdata","example_gtf.gtf", package = "GeneStructureTools")) exons <- gtf[gtf$type=="exon"] g <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10 leafcutterTranscriptChangeSummary(significantEvents = leafcutterIntrons, exons=exons,BSgenome = g,NMD=FALSE)