getFeatureRanges: Generate a GRangesList object with feature ranges
In eisaR: Exon-Intron Split Analysis (EISA) in R

Description Usage Arguments Value Author(s) Examples

Generate a GRangesList object with genomic ranges for (any combination of) spliced transcripts, unspliced transcripts and introns.

getFeatureRanges(
  gtf,
  featureType = c("spliced", "intron"),
  intronType = "separate",
  flankLength = 90L,
  joinOverlappingIntrons = FALSE,
  verbose = TRUE
)

`gtf`	Path to gtf file.
`featureType`	Character vector indicating the type(s) of features to extract, any subset of `c("spliced", "intron", "unspliced")`.
`intronType`	Character vector indicating how to define the introns (only used if "intron" is part of `featureType`). Has to be either "separate" (introns are defined for each transcript separately) or "collapse" (transcripts of the same gene are first collapsed before introns are defined as any non-exonic part of the gene locus).
`flankLength`	Integer scalar indicating the length of the flanking sequence added to each side of each extracted intron (only used if "intron" is included in `featureType`).
`joinOverlappingIntrons`	Logical scalar indicating whether two introns that overlap (after adding the flanking sequences) should be joined into one feature.
`verbose`	Logical scalar, whether to print out progress messages.

Returns a GRangesList object where each element represents one extracted feature. The metadata of this object contains two data.frames mapping corresponding identifiers between the different feature types, as well as a list of all features for each type.

Charlotte Soneson

  ## Get feature ranges
  grl <- getFeatureRanges(
    gtf = system.file("extdata/small_example.gtf", package = "eisaR"),
    featureType = c("spliced", "intron"),
    intronType = "separate",
    flankLength = 5L,
    joinOverlappingIntrons = FALSE,
    verbose = TRUE
  )
  
  ## GRangesList
  grl
  
  ## Corresponding transcript/gene IDs
  S4Vectors::metadata(grl)$corrtx
  S4Vectors::metadata(grl)$corrgene
  
  ## List of features of different types
  S4Vectors::metadata(grl)$featurelist
  
  ## Get feature sequences
  if (requireNamespace("BSgenome", quietly = TRUE)) {
    library(BSgenome)
    genome <- Biostrings::readDNAStringSet(
      system.file("extdata/small_example_genome.fa", package = "eisaR"))
    seqs <- GenomicFeatures::extractTranscriptSeqs(x = genome, 
                                                   transcripts = grl)
    seqs
  }