R/annotateASevents.R

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

#' AS event annotation
#'
#' Detect and annotate AS events from GTF. This function borrows code
#' from the \code{IVAS} package.
#'
#' @param object Object of class ASpediaFI
#' @param gtf.file an input GTF file
#' @param num.cores the number of cores for parallel processing
#' @export
#' @importFrom rtracklayer import.gff
#' @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.
#' @return ASpediaFI object with a list of AS event annotations
#' @examples
#' fi <- new('ASpediaFI')
#' gtf <- system.file('extdata/GRCh38.subset.gtf', package = 'ASpediaFI')
#' fi <- annotateASevents(fi, gtf.file = gtf, num.cores = 1)
#' sapply(events(fi), length)
#' head(events(fi)$SE)
annotateASevents <- function(object, gtf.file, num.cores = 1) {
    outFI <- object
    as.list <- detect(gtf.file, num.cores)
    gtf(outFI) <- import.gff(gtf.file)
    events(outFI) <- annotate(as.list, gtf(outFI))
    return(outFI)
}