alternativeIntronUsage: Create transcripts with alternative intron usage

Description Usage Arguments Value Author(s) See Also Examples

View source: R/leafCutter.R

Description

Creates transcript isoforms from alternative intron usage tested by leafcutter

Usage

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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

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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.