alternativeIntronUsage {GeneStructureTools} | R Documentation |
Creates transcript isoforms from alternative intron usage tested by leafcutter
alternativeIntronUsage(altIntronLocs, exons)
altIntronLocs |
data.frame containing information from the per_intron_results.tab file output from leafcutter. Note that only one cluster of alternative introns can be processed at a time. |
exons |
GRanges object made from a GTF with ONLY exon annotations (no gene, transcript, CDS etc.) |
GRanges object with all potential alternative isoforms skipping the introns specified in either the upregulated or downregulated locations
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$type=="exon"] # single cluster processing cluster <- leafcutterIntrons[leafcutterIntrons$cluster=="chr16:clu_1396",] altIsoforms1396 <- alternativeIntronUsage(cluster, exons) unique(altIsoforms1396$transcript_id) cluster <- leafcutterIntrons[leafcutterIntrons$cluster=="chr16:clu_1395",] altIsoforms1395 <- alternativeIntronUsage(cluster, exons) unique(altIsoforms1395$transcript_id) # multiple cluster processing altIsoforms1396plus1395 <- alternativeIntronUsage(cluster, c(exons, altIsoforms1396)) unique(altIsoforms1396plus1395$transcript_id)