Export GRangesList to GTF

Export the features in a GRangesList generated by getFeatureRanges to a GTF file. The function will represent each row of each of the entries as an "exon", each individual entry as a "transcript", and aggregate all features belonging to the same gene as a "gene" entry in the GTF file.

exportToGtf(grl, filepath)

Arguments

grl

GRangesList object, typically generated by getFeatureRanges

filepath

Path to output GTF file

Value

Does not return anything, generates a GTF file

Author

Charlotte Soneson

Examples

  ## 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
  )
#> Import genomic features from the file as a GRanges object ... 
#> OK
#> Prepare the 'metadata' data frame ... 
#> OK
#> Make the TxDb object ... 
#> OK
#> 'select()' returned 1:1 mapping between keys and columns
#> Extracting spliced transcript features
#> Extracting introns using the separate approach
  
  ## Export GTF
  exportToGtf(grl = grl, filepath = file.path(tempdir(), "exported.gtf"))