alternativeIntronUsage {GeneStructureTools} | R Documentation

## Create transcripts with alternative intron usage

### Description

Creates transcript isoforms from alternative intron usage tested by leafcutter

### Usage

    alternativeIntronUsage(altIntronLocs, exons)

### Arguments

`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.)

### Value

GRanges object with all potential alternative isoforms skipping the introns specified in either the upregulated or downregulated locations

### Author(s)

Beth Signal

### Examples

    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)

[Package GeneStructureTools version 1.4.0 Index]