R/mapTranscriptsMXEevent.R

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

#' Map transcripts to MXE events
#'
#' This function maps transcripts to MXE events
#'
#' @param eventGr A GRangesList object of AS event
#' @param gtf_exons A GRanges object containing exons in gtf
#' @return a list of transcripts
#' @details This function is borrowed from the \code{maser} package.
#' @references Veiga, D. (2019). maser: Mapping Alternative Splicing Events
#' to pRoteins. R package version 1.2.0. https://github.com/DiogoVeiga/maser
#' @keywords internal
#' @importFrom GenomicRanges findOverlaps GRanges
#' @importFrom IRanges IRanges
#' @importFrom S4Vectors subjectHits
#' @noRd
mapTranscriptsMXEevent <- function(eventGr, gtf_exons) {
    ovl.e1 <- findOverlaps(eventGr$exon_1, gtf_exons, type = "equal")
    ovl.e2 <- findOverlaps(eventGr$exon_2, gtf_exons, type = "equal")
    ovl.e3 <- findOverlaps(eventGr$exon_upstream, gtf_exons, type = "equal")
    ovl.e4 <- findOverlaps(eventGr$exon_downstream, gtf_exons, type = "equal")
    mytx.ids.e1 <- gtf_exons$transcript_id[subjectHits(ovl.e1)]
    mytx.ids.e2 <- gtf_exons$transcript_id[subjectHits(ovl.e2)]
    mytx.ids.e3 <- gtf_exons$transcript_id[subjectHits(ovl.e3)]
    mytx.ids.e4 <- gtf_exons$transcript_id[subjectHits(ovl.e4)]
    intron.mxe.exon1 <- GRanges(seqnames = seqnames(eventGr$exon_1),
                    ranges = IRanges(start = c(end(eventGr$exon_upstream) + 1,
                    end(eventGr$exon_1) + 1),
                    end = c(start(eventGr$exon_1) - 1,
                    start(eventGr$exon_downstream) - 1)),
                    strand = strand(eventGr$exon_1))
    intron.mxe.exon2 <- GRanges(seqnames = seqnames(eventGr$exon_2),
                    ranges = IRanges(start = c(end(eventGr$exon_upstream) + 1,
                    end(eventGr$exon_2) + 1),
                    end = c(start(eventGr$exon_2) - 1,
                    start(eventGr$exon_downstream) - 1)),
                    strand = strand(eventGr$exon_2))
    ovl.mxe.exon1 <- findOverlaps(intron.mxe.exon1, gtf_exons, type = "any")
    mytx.ids.intron1 <- gtf_exons$transcript_id[subjectHits(ovl.mxe.exon1)]
    ovl.mxe.exon2 <- findOverlaps(intron.mxe.exon2, gtf_exons, type = "any")
    mytx.ids.intron2 <- gtf_exons$transcript_id[subjectHits(ovl.mxe.exon2)]

    mytx.ids.mxe.exon1 <- intersect(mytx.ids.e3, mytx.ids.e4)
    mytx.ids.mxe.exon1 <- intersect(mytx.ids.mxe.exon1, mytx.ids.e1)
    mytx.ids.mxe.exon2 <- intersect(mytx.ids.e3, mytx.ids.e4)
    mytx.ids.mxe.exon2 <- intersect(mytx.ids.mxe.exon2, mytx.ids.e2)

    mytx.ids.mxe.exon1 <- setdiff(mytx.ids.mxe.exon1, mytx.ids.intron1)
    mytx.ids.mxe.exon2 <- setdiff(mytx.ids.mxe.exon2, mytx.ids.intron2)
    tx_ids <- list()
    tx_ids[["txn_mxe_exon1"]] <- mytx.ids.mxe.exon1
    tx_ids[["txn_mxe_exon2"]] <- mytx.ids.mxe.exon2
    return(tx_ids)
}