R/annotate.R

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

#' AS event annotation
#'
#' This function converts information of AS events into ASpedia format.
#'
#' @param ASlist a list of AS events
#' @param gtf a GRanges object representing GTF
#' @return A list of annotated AS events
#' @keywords internal
#' @importFrom limma strsplit2
#' @noRd
annotate <- function(ASlist, gtf) {
    a5ss <- ASlist$A5SS
    a3ss <- ASlist$A3SS
    se <- ASlist$SE
    mxe <- ASlist$MXE
    ri <- ASlist$RI

    id_to_name <- data.frame(id = gtf$gene_id, name = gtf$gene_name,
                                stringsAsFactors = FALSE)
    id_to_name <- unique(id_to_name)
    rownames(id_to_name) <- id_to_name$id

    # Annotate A5SS events
    if (length(a5ss)) {
        short.start <- strsplit2(a5ss[, "ShortEX"], split = "-")[, 1]
        short.end <- strsplit2(a5ss[, "ShortEX"], split = "-")[, 2]
        long.start <- strsplit2(a5ss[, "LongEX"], split = "-")[, 1]
        long.end <- strsplit2(a5ss[, "LongEX"], split = "-")[, 2]
        nei.start <- strsplit2(a5ss[, "NeighborEX"], split = "-")[, 1]
        nei.end <- strsplit2(a5ss[, "NeighborEX"], split = "-")[, 2]
        gene.symbol <- id_to_name[a5ss[, "EnsID"], "name"]

        aspedia.id <- ifelse(a5ss[, "Strand"] == "+",
                            paste(gene.symbol,
                                "A5SS", a5ss[, "Nchr"], long.start,
                                short.end, long.end, nei.start,
                                nei.end, sep = ":"),
                            paste(gene.symbol, "A5SS", a5ss[, "Nchr"],
                                    long.end, short.start, long.start,
                                    nei.end, nei.start, sep = ":"))

        a5ss <- rbind(cbind(a5ss, EventID = aspedia.id))
        rownames(a5ss) <- seq_len(nrow(a5ss))
    }

    # Annotate A3SS events
    if (length(a3ss)) {
        short.start <- strsplit2(a3ss[, "ShortEX"], split = "-")[, 1]
        short.end <- strsplit2(a3ss[, "ShortEX"], split = "-")[, 2]
        long.start <- strsplit2(a3ss[, "LongEX"], split = "-")[, 1]
        long.end <- strsplit2(a3ss[, "LongEX"], split = "-")[, 2]
        nei.start <- strsplit2(a3ss[, "NeighborEX"], split = "-")[, 1]
        nei.end <- strsplit2(a3ss[, "NeighborEX"], split = "-")[, 2]
        gene.symbol <- id_to_name[a3ss[, "EnsID"], "name"]

        aspedia.id <- ifelse(a3ss[, "Strand"] == "+",
                                paste(gene.symbol, "A3SS", a3ss[, "Nchr"],
                                        nei.start, nei.end, long.start,
                                        short.start, long.end, sep = ":"),
                                paste(gene.symbol, "A3SS", a3ss[, "Nchr"],
                                        nei.end, nei.start, long.end, short.end,
                                        long.start, sep = ":"))

        a3ss <- rbind(cbind(a3ss, EventID = aspedia.id))
        rownames(a3ss) <- seq_len(nrow(a3ss))
    }

    # Annotate SE events
    if (length(se)) {
        first.start <- strsplit2(se[, "1stEX"], split = "-")[, 1]
        first.end <- strsplit2(se[, "1stEX"], split = "-")[, 2]
        up.start <- strsplit2(se[, "UpEX"], split = "-")[, 1]
        up.end <- strsplit2(se[, "UpEX"], split = "-")[, 2]
        down.start <- strsplit2(se[, "DownEX"], split = "-")[, 1]
        down.end <- strsplit2(se[, "DownEX"], split = "-")[, 2]
        gene.symbol <- id_to_name[se[, "EnsID"], "name"]

        aspedia.id <- ifelse(se[, "Strand"] == "+",
                                paste(gene.symbol, "SE", se[, "Nchr"],
                                        down.start, down.end, first.start,
                                        first.end, up.start, up.end, sep = ":"),
                                paste(gene.symbol, "SE", se[, "Nchr"], up.end,
                                        up.start, first.end, first.start,
                                        down.end, down.start, sep = ":"))

        se <- rbind(cbind(se, EventID = aspedia.id))
        rownames(se) <- seq_len(nrow(se))
    }

    # Annotate MXE events
    if (length(mxe)) {
        first.start <- strsplit2(mxe[, "1stEX"], split = "-")[, 1]
        first.end <- strsplit2(mxe[, "1stEX"], split = "-")[, 2]
        second.start <- strsplit2(mxe[, "2ndEX"], split = "-")[, 1]
        second.end <- strsplit2(mxe[, "2ndEX"], split = "-")[, 2]
        up.start <- strsplit2(mxe[, "UpEX"], split = "-")[, 1]
        up.end <- strsplit2(mxe[, "UpEX"], split = "-")[, 2]
        down.start <- strsplit2(mxe[, "DownEX"], split = "-")[, 1]
        down.end <- strsplit2(mxe[, "DownEX"], split = "-")[, 2]
        gene.symbol <- id_to_name[mxe[, "EnsID"], "name"]

        aspedia.id <- ifelse(mxe[, "Strand"] == "+",
                                paste(gene.symbol, "MXE", mxe[, "Nchr"],
                                    down.start, down.end, first.start,
                                    first.end, second.start, second.end,
                                    up.start, up.end, sep = ":"),
                                paste(gene.symbol, "MXE", mxe[, "Nchr"],
                                    up.end, up.start, second.end, second.start,
                                    first.end, first.start, down.end,
                                    down.start, sep = ":"))

        mxe <- rbind(cbind(mxe, EventID = aspedia.id))
        rownames(mxe) <- seq_len(nrow(mxe))
    }

    # Annotate RI events
    if (length(ri)) {
        up.start <- strsplit2(ri[, "UpEX"], split = "-")[, 1]
        up.end <- strsplit2(ri[, "UpEX"], split = "-")[, 2]
        down.start <- strsplit2(ri[, "DownEX"], split = "-")[, 1]
        down.end <- strsplit2(ri[, "DownEX"], split = "-")[, 2]
        re.start <- strsplit2(ri[, "RetainEX"], split = "-")[, 1]
        re.end <- strsplit2(ri[, "RetainEX"], split = "-")[, 2]
        gene.symbol <- id_to_name[ri[, "EnsID"], "name"]

        aspedia.id <- ifelse(ri[, "Strand"] == "+",
                                paste(gene.symbol, "RI", ri[, "Nchr"],
                                    down.start, down.end, up.start,
                                    up.end, sep = ":"),
                                paste(gene.symbol, "RI", ri[, "Nchr"],
                                    up.end, up.start, down.end, down.start,
                                    sep = ":"))

        ri <- rbind(cbind(ri, EventID = aspedia.id))
        rownames(ri) <- seq_len(nrow(ri))
    }

    return(list(A5SS = a5ss, A3SS = a3ss, SE = se, MXE = mxe, RI = ri))
}