R/parse_gtf.R

In TRON-Bioinformatics/splice2neo: Aberrant splice junction analysis with associated mutations

#' Parse a GFF/GTF file as \code{\link[GenomicRanges]{GRangesList}} of exons
#'
#' @param file path to a GFF or GTF file (See \code{\link[GenomicFeatures]{makeTxDbFromGFF}}))
#' @param ... other options passed to file path to \code{\link[GenomicFeatures]{makeTxDbFromGFF}})
#' @return A \code{\link[GenomicRanges]{GRangesList}} of exons grouped by transcripts
#'
#' @examples
#' gff_file <- system.file("extdata","GFF3_files","a.gff3",package="splice2neo")
#'
#' parse_gtf(gff_file)
#'
#' @export
parse_gtf <- function(file, ...){

  txdb <- suppressWarnings(GenomicFeatures::makeTxDbFromGFF(file, ...))
  transcripts <- GenomicFeatures::exonsBy(txdb, by = c("tx"), use.names = TRUE)

  return(transcripts)
}