calculate_exon_couplings.R

#' Calculate exon couplings
#'
#' @param junctions: junctions obtained from Long read data assigned to read_ids
#' @param reference_junctions: set of junctions of interest classified using SaiLoR
#'
#' @return couplings result list file with couplings for TSS and TES
#' @export
#'
#' @examples
calculate_exon_couplings <- function(junctions,reference_junctions){
  couplingsResult <- list()
  res_couplings_tss <- compute_exon_tss_couplings(junctions,reference_junctions)
  res_couplings_tes <- compute_exon_3end_couplings(junctions,reference_junctions)
  couplingsResult$TSS <- res_couplings_tss
  couplingsResult$TES <- res_couplings_tes
  couplingsResult <- unlist(couplingsResult, recursive = FALSE)
  return(couplingsResult)
}