R/detect.R

In ASpediaFI: ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events

#' Detection of AS events
#'
#' This function detects AS events from an input GTF.
#'
#' @param gtf.file an input GTF or GFF3 file.
#' @param num.cores the number of cores for parallel processing
#' @return A list of AS events
#' @details This function wraps around \code{makeTxDbFromGFF} in the
#' \code{GenomicFeatures} package and \code{Splicingfinder} in the
#' \code{IVAS} package.
#' @references Han, S. et al. (2017). Genome wide discovery of genetic variants
#' affecting alternative splicing patterns in human using bioinformatics method.
#' \emph{Genes & Genomics}, 39.
#' @import GenomicFeatures
#' @importFrom biomaRt select
#' @keywords internal
#' @noRd
detect <- function(gtf.file, num.cores) {
    gtfdb <- makeTxDbFromGFF(gtf.file)
    total.exon.range <- exonsBy(gtfdb, by = "tx")
    total.intron.range <- intronsByTranscript(gtfdb)
    txTable <- select(gtfdb, keys = names(total.exon.range),
                        columns = c("TXCHROM", "TXNAME", "GENEID",
                                        "TXSTART", "TXEND", "TXSTRAND"),
                        keytype = "TXID")
    aslist.raw <- detectEventFromTxDb(gtfdb, num.cores)
    aslist.filtered <- filterEvent(aslist.raw, total.exon.range,
                                    total.intron.range, txTable)
    return(aslist.filtered)
}