alternativeIntronUsage: Create transcripts with alternative intron usage

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

Description

Creates transcript isoforms from alternative intron usage tested by leafcutter

Usage

alternativeIntronUsage(
  altIntronLocs,
  exons,
  replaceInternalExons = TRUE,
  junctions = NULL
)

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.)
replaceInternalExons	replace any internal transcript exons with inferred exons from multi-intron leafcutter intron sets?
junctions	GRanges object from readLeafcutterJunctions()

Value

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

Author(s)

Beth Signal

See Also

Other leafcutter splicing isoform creation: leafcutterIntronsToExons(), makeNewLeafExonsUnanchored(), makeNewLeafExons(), readLeafcutterJunctions()

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$type == "exon"]
# single cluster processing
cluster <- leafcutterIntrons[leafcutterIntrons$cluster == "chr17:clu_20975_+", ]
altIsoforms20975 <- alternativeIntronUsage(cluster, exons)
unique(altIsoforms20975$transcript_id)

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