R/createAnnotationTrack_transcripts.R

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

#' Create transcript tracks from AS event
#'
#' This function creates transcript tracks from AS event.
#'
#' @param eventGr A GRangesList object of AS event
#' @param gtf_exons A GRanges object containing exons in gtf
#' @param type AS event type
#' @return a list of GeneRegionTrack objects
#' @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
#' @noRd
createAnnotationTrack_transcripts <- function(eventGr, gtf_exons, type) {
    if (type == "A3SS") {
        if (as.character(strand(eventGr[1])) == "+") {
            tx_ids <- mapTranscriptsA3SSevent(eventGr, gtf_exons)
        } else {
            tx_ids <- mapTranscriptsA5SSevent(eventGr, gtf_exons)
        }
        res.df <- createExonTable(gtf_exons, tx_ids$txn_short)
        skippingTrack <- createTxnTrack(res.df, "A3SS Short", "A3SS_Short")
        res.df <- createExonTable(gtf_exons, tx_ids$txn_long)
        inclusionTrack <- createTxnTrack(res.df, "A3SS Long", "A3SS_Long")
        txn_tracks <- list(inclusionTrack = inclusionTrack,
                            skippingTrack = skippingTrack)
        return(txn_tracks)
    }
    if (type == "A5SS") {
        if (as.character(strand(eventGr[1])) == "+") {
            tx_ids <- mapTranscriptsA5SSevent(eventGr, gtf_exons)
        } else {
            tx_ids <- mapTranscriptsA3SSevent(eventGr, gtf_exons)
        }
        res.df <- createExonTable(gtf_exons, tx_ids$txn_short)
        skippingTrack <- createTxnTrack(res.df, "A5SS Short", "A5SS_Short")
        res.df <- createExonTable(gtf_exons, tx_ids$txn_long)
        inclusionTrack <- createTxnTrack(res.df, "A5SS Long", "A5SS_Long")
        txn_tracks <- list(inclusionTrack = inclusionTrack, skippingTrack =
                                skippingTrack)
        return(txn_tracks)
    }
    if (type == "SE") {
        tx_ids <- mapTranscriptsSEevent(eventGr, gtf_exons)
        res.df <- createExonTable(gtf_exons, tx_ids$txn_3exons)
        inclusionTrack <- createTxnTrack(res.df, "Inclusion", "Inclusion")
        res.df <- createExonTable(gtf_exons, tx_ids$txn_2exons)
        skippingTrack <- createTxnTrack(res.df, "Skipping", "Skipping")
        txn_tracks <- list(inclusionTrack = inclusionTrack, skippingTrack =
                                skippingTrack)
        return(txn_tracks)
    }
    if (type == "MXE") {
        tx_ids <- mapTranscriptsMXEevent(eventGr, gtf_exons)
        res.df <- createExonTable(gtf_exons, tx_ids$txn_mxe_exon1)
        inclusionTrack <- createTxnTrack(res.df, "MXE Exon 1", "MXE_Exon1")
        res.df <- createExonTable(gtf_exons, tx_ids$txn_mxe_exon2)
        skippingTrack <- createTxnTrack(res.df, "MXE Exon 2", "MXE_Exon2")
        txn_tracks <- list(inclusionTrack = inclusionTrack, skippingTrack =
                                skippingTrack)
        return(txn_tracks)
    }
    if (type == "RI") {
        tx_ids <- mapTranscriptsRIevent(eventGr, gtf_exons)
        res.df <- createExonTable(gtf_exons, tx_ids$txn_retention)
        retention_Track <- createTxnTrack(res.df, "Retention", "Retention")
        res.df <- createExonTable(gtf_exons, tx_ids$txn_nonRetention)
        nonRetention_Track <- createTxnTrack(res.df, "Non-retention",
                                                "Non_Retention")
        txn_tracks <- list(inclusionTrack = retention_Track, skippingTrack =
                                nonRetention_Track)
    }
}