R/detectSEandMXE.R

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

#' Detection of skipped and mutually exclusive exons
#'
#' This function detects skipped (SE) and mutually exclusive exons (MXE) events.
#'
#' @param exon.info A matrix containing exon locus
#' @param intron.info A matrix containing intron locus
#' @param alt.intron.info A matrix containing flanking introns of
#' alternative exons
#' @return A matrix containing SE and MXE events
#' @details This function is borrowed from 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.
#' @keywords internal
#' @noRd
#' @importFrom stats complete.cases
detectSEandMXE <- function(exon.info, intron.info, alt.intron.info) {
    tx.exon.ranges <- cbind(tapply(exon.info[, "start"], rownames(exon.info),
                                    min),
                            tapply(exon.info[, "start"], rownames(exon.info),
                                    max))
    colnames(tx.exon.ranges) <- c("start", "end")
    alt.intron.info <- alt.intron.info[1, ]
    fi.exon.num <- grep(alt.intron.info["start"] - 1, exon.info[, "end"])
    se.exon.num <- grep(alt.intron.info["end"] + 1, exon.info[, "start"])
    SE.EX <- NULL
    for (i in seq_len(length(fi.exon.num))) {
        fi.exon <- exon.info[fi.exon.num[i], ]
        if (length(which(fi.exon["start"] > intron.info[, "start"] - 1 &
                            fi.exon["end"] < intron.info[, "end"] - 1)) != 0) {
            SE.EX <- rbind(SE.EX, fi.exon)
        }
    }
    for (i in seq_len(length(se.exon.num))) {
        se.exon <- exon.info[se.exon.num[i], ]
        if (length(which(se.exon["start"] > intron.info[, "start"] - 1 &
                    se.exon["end"] < intron.info[, "end"] - 1)) != 0) {
            SE.EX <- rbind(SE.EX, se.exon)
        }
    }
    if (length(SE.EX) == 0) {
        return(NULL)
    }
    SE.EX <- rbind(SE.EX[SE.EX[, "start"] != SE.EX[, "end"], ])
    if (length(SE.EX) == 0) {
        return(NULL)
    }
    SE.EX <- unique(SE.EX)
    get.test.tx <- function(tx.cal) {
        each.tx.cal <- as.double(strsplit(tx.cal, "-")[[1]])
        each.test.tx <- rownames(tx.exon.ranges)[tx.exon.ranges[, "start"] <
                    each.tx.cal[1] & tx.exon.ranges[, "end"] > each.tx.cal[2]]
    }
    test.tx <- unique(unlist(lapply(paste(SE.EX[, "start"], SE.EX[, "end"],
                                                    sep = "-"), get.test.tx)))
    exon.info <- rbind(exon.info[is.element(rownames(exon.info), test.tx), ])
    if (nrow(exon.info) == 1) {
        rownames(exon.info) <- test.tx
    }
    intron.info <- rbind(intron.info[is.element(rownames(intron.info),
                                                                test.tx), ])
    if (nrow(intron.info) == 1) {
        rownames(intron.info) <- test.tx
    }
    rownames(SE.EX) <- seq_len(nrow(SE.EX))
    get.ES.int.num <- function(tx.cal) {
        each.tx.se <- as.double(strsplit(tx.cal, "-")[[1]])
        int.num <- which(intron.info[, "start"] + 1 < each.tx.se[1] &
                                    intron.info[, "end"] - 1 > each.tx.se[2])
        int.num
    }
    ES.int.num <- unique(unlist(lapply(paste(SE.EX[, "start"], SE.EX[, "end"],
                                                sep = "-"), get.ES.int.num)))
    if (length(ES.int.num) == 0) {
        return(NULL)
    }
    ES.int.mat <- cbind(as.double(rownames(intron.info)[ES.int.num]),
                                            rbind(intron.info[ES.int.num, ]))
    rm.int.num <- NULL
    for (i in seq_len(nrow(ES.int.mat))) {
        num.over.exons <- rownames(exon.info)[exon.info[, "start"] >
                                                ES.int.mat[i, "start"] - 1 &
                                                exon.info[, "end"] <
                                                ES.int.mat[i, "end"] + 1]
        t.num.over.exons <- table(num.over.exons)
        if (length(which(t.num.over.exons > 2)) != 0) {
            rm.int.num <- c(rm.int.num, i)
        }
    }
    if (length(rm.int.num) != 0) {
        ES.int.mat <- rbind(ES.int.mat[-rm.int.num, ])
    }
    if (length(ES.int.mat) == 0) {
        return(NULL)
    }
    colnames(ES.int.mat) <- c("txid", "start", "end")
    min.int <- min(ES.int.mat[, "start"])
    max.int <- max(ES.int.mat[, "end"])
    final.SE.num <- which(exon.info[, "start"] > min.int - 1 &
                            exon.info[, "end"] < max.int + 1)
    final.SE.EX <- cbind(as.double(rownames(exon.info)[final.SE.num]),
                            rbind(exon.info[final.SE.num, ]))
    colnames(final.SE.EX) <- c("txid", "start", "end")
    get.ES.int.num2 <- function(fse) {
        each.fse <- as.double(strsplit(fse, "-")[[1]])
        names(each.fse) <- c("start", "end")
        which(intron.info[, "start"] + 1 < each.fse["start"] &
            intron.info[, "end"] - 1 > each.fse["end"])
    }
    ES.int.num <- lapply(paste(final.SE.EX[, "start"], final.SE.EX[, "end"],
                            sep = "-"), get.ES.int.num2)
    ES.int.num <- unique(unlist(ES.int.num))
    ES.int.mat <- cbind(as.double(rownames(intron.info)[ES.int.num]),
                            rbind(intron.info[ES.int.num, ]))
    colnames(ES.int.mat) <- c("txid", "start", "end")
    colnames(final.SE.EX) <- c("txid", "start", "end")
    final.SE.EX <- rbind(final.SE.EX[is.element(final.SE.EX[, "txid"],
                            as.double(test.tx)), ])
    t.final.SE.EX <- table(final.SE.EX[, "txid"])
    up2.txid <- as.double(names(t.final.SE.EX)[t.final.SE.EX > 2])
    up1.txid <- as.double(names(t.final.SE.EX)[t.final.SE.EX == 2])
    if (length(ES.int.mat) == 0 | length(final.SE.EX) == 0) {
        return(NULL)
    }
    get.alt.result <- function(total.ES.int) {
        ES.int <- as.double(strsplit(total.ES.int, "-")[[1]])
        names(ES.int) <- colnames(ES.int.mat)
        alt.ex <- exon.info[rownames(exon.info) == ES.int["txid"] &
                            (exon.info[, "end"] == ES.int["start"] - 1 |
                                exon.info[, "start"] == ES.int["end"] + 1), ]
        alt.ex.result <- cbind(paste(alt.ex[, "start"], alt.ex[, "end"],
                                        sep = "-"))
    }
    alt.result <- lapply(paste(ES.int.mat[, 1], ES.int.mat[, 2],
                                ES.int.mat[, 3], sep = "-"), get.alt.result)
    pre.alt.result <- NULL
    if (length(alt.result) != 0) {
        for (i in seq_len(length(alt.result))) {
            pre.alt.result <- rbind(pre.alt.result,
                                    cbind(alt.result[[i]][1],
                                    alt.result[[i]][2]))
        }
    }
    pre.alt.result <- pre.alt.result[!is.element(pre.alt.result[, 1],
                        paste(final.SE.EX[, "start"], final.SE.EX[, "end"],
                            sep = "-")) & !is.element(pre.alt.result[, 2],
                        paste(final.SE.EX[, "start"], final.SE.EX[, "end"],
                            sep = "-")), ]
    alt.result <- rbind(unique(pre.alt.result))
    alt.result <- alt.result[complete.cases(alt.result), , drop = FALSE]
    skipped.flank.ex <- alt.result
    up2.es.mat <- NULL
    up2.es.mat.2 <- NULL
    if (length(up1.txid) != 0) {
        for (i in seq_len(length(up1.txid))) {
            up1.final.SE.EX <- final.SE.EX[final.SE.EX[, "txid"] ==
                                            up1.txid[i], ]
            min.start <- as.double(min(up1.final.SE.EX[, "start"]))
            max.end <- as.double(max(up1.final.SE.EX[, "end"]))
            le.int <- intron.info[rownames(intron.info) == up1.txid[i] &
                                    intron.info[, "end"] == min.start - 1,
                                    "start"] - 1
            ri.int <- intron.info[rownames(intron.info) == up1.txid[i] &
                                    intron.info[, "start"] == max.end + 1,
                                    "end"] + 1
            le.ex <- unique(rbind(exon.info[rownames(exon.info) == up1.txid[i] &
                                exon.info[, "end"] == le.int, ]))
            ri.ex <- unique(rbind(exon.info[rownames(exon.info) == up1.txid[i] &
                                exon.info[, "start"] == ri.int, ]))
            le.ex <- paste(le.ex[, "start"], le.ex[, "end"], sep = "-")
            ri.ex <- paste(ri.ex[, "start"], ri.ex[, "end"], sep = "-")
            le.ex.des <- paste(sort(unique(paste(exon.info[exon.info[, "end"] ==
                                le.int, "start"],
                                exon.info[exon.info[, "end"] == le.int, "end"],
                                sep = "-"))), collapse = ",")
            ri.ex.des <- paste(sort(unique(paste(
                            exon.info[exon.info[, "start"] == ri.int, "start"],
                            exon.info[exon.info[, "start"] == ri.int, "end"],
                            sep = "-"))), collapse = ",")
            if (length(le.ex) != 0 & length(ri.ex) != 0) {
                targets.exs <- rbind(c(paste(up1.final.SE.EX[1, -1],
                                    collapse = "-"),
                                    paste(up1.final.SE.EX[2, -1],
                                    collapse = "-")))
                up2.es.mat <- rbind(up2.es.mat, cbind(targets.exs,
                                    paste(le.ex, collapse = ","),
                                    paste(ri.ex, collapse = ","),
                                    targets.exs, le.ex.des, ri.ex.des, "SE"))
                if (length(alt.result) != 0) {
                    up2.es.mat.2 <- cbind(paste(up1.final.SE.EX[1, -1],
                                            collapse = "-"),
                                            paste(up1.final.SE.EX[2, -1],
                                            collapse = "-"),
                                            rbind(alt.result), "SE")
                }
            }
        }
    }
    get.inclu.flack.ex <- function(total.in.ex) {
        in.ex <- as.double(strsplit(total.in.ex, "-")[[1]])
        names(in.ex) <- c("txid", "start", "end")
        ES.mat.2 <- NULL
        if (length(alt.result) != 0) {
            ES.mat.2 <- cbind(paste(in.ex[-1], collapse = "-"), "NA",
                                alt.result, "SE")
        }
        ES.mat.2 <- rbind(ES.mat.2, up2.es.mat.2)
        if (length(ES.mat.2) != 0) {
            get.ES.mat.2 <- function(each.num) {
                each.ES.mat.2 <- ES.mat.2[each.num, ]
                pre.do.des <- unique(rbind(exon.info[exon.info[, "end"] ==
                                unlist(strsplit(each.ES.mat.2[3], "-"))[2], ]))
                pre.up.des <- unique(rbind(exon.info[exon.info[, "start"] ==
                                unlist(strsplit(each.ES.mat.2[4], "-"))[1], ]))
                each.ES.mat.2.do.des <- paste(sort(paste(pre.do.des[, "start"],
                                            pre.do.des[, "end"], sep = "-")),
                                            collapse = ",")
                each.ES.mat.2.up.des <- paste(sort(paste(pre.up.des[, "start"],
                                            pre.up.des[, "end"], sep = "-")),
                                            collapse = ",")
                c(each.ES.mat.2[-5], each.ES.mat.2[seq_len(2)],
                    each.ES.mat.2.do.des, each.ES.mat.2.up.des,
                    each.ES.mat.2[5])
            }
            ES.mat.2 <- do.call(rbind, lapply(seq_len(nrow(ES.mat.2)),
                                get.ES.mat.2))
        }
        le.intron <- rbind(intron.info[intron.info[, "end"] + 1 ==
                            in.ex["start"], ])
        le.exon.num <- is.element(exon.info[, "end"], le.intron[, "start"] - 1)
        le.exon <- cbind(rownames(exon.info)[le.exon.num],
                            rbind(exon.info[le.exon.num, ]))
        colnames(le.exon) <- c("txnum", "le.start", "le.end")
        ri.intron <- rbind(intron.info[intron.info[, "start"] - 1 ==
                            in.ex["end"], ])
        ri.exon.num <- is.element(exon.info[, "start"], ri.intron[, "end"] + 1)
        ri.exon <- cbind(rownames(exon.info)[ri.exon.num],
                            rbind(exon.info[ri.exon.num, ]))
        colnames(ri.exon) <- c("txnum", "ri.start", "ri.end")
        inExTx <- in.ex["txid"]
        le.exon <- rbind(le.exon[is.element(le.exon[, "txnum"], inExTx), ])
        ri.exon <- rbind(ri.exon[is.element(ri.exon[, "txnum"], inExTx), ])
        le.ri.exon <- unique(S4Vectors::merge(le.exon, ri.exon, by.x = "txnum",
                                                by.y = "txnum")[, 2:5])
        if (nrow(le.ri.exon) != 0) {
            get.ES.result <- function(ex.nums) {
                each.le.ri.exon <- rbind(le.ri.exon[ex.nums, ])
                le.des <- unique(rbind(exon.info[exon.info[, "end"] ==
                                    each.le.ri.exon[, "le.end"], ]))
                ri.des <- unique(rbind(exon.info[exon.info[, "start"] ==
                                    each.le.ri.exon[, "ri.start"], ]))
                p.le.des <- paste(sort(paste(le.des[, "start"], le.des[, "end"],
                                    sep = "-")), collapse = ",")
                p.ri.des <- paste(sort(paste(ri.des[, "start"], ri.des[, "end"],
                                    sep = "-")), collapse = ",")
                cbind(paste(in.ex[-1], collapse = "-"),
                            paste(each.le.ri.exon[, "le.start"],
                            each.le.ri.exon[, "le.end"], sep = "-"),
                        paste(each.le.ri.exon[, "ri.start"],
                                each.le.ri.exon[, "ri.end"], sep = "-"),
                        paste(in.ex[-1], collapse = "-"), "NA", p.le.des,
                                p.ri.des, "SE")
            }
            ES.result <- do.call(rbind, lapply(seq_len(nrow(le.ri.exon)),
                                    get.ES.result))
            ES.result <- cbind(ES.result[, 1], "NA", rbind(ES.result[, -1]))
            ES.result <- rbind(ES.result, up2.es.mat)
            final.ES.result <- NULL
            if (length(ES.mat.2) != 0) {
                for (i in seq_len(nrow(ES.result))) {
                    for (j in seq_len(nrow(ES.mat.2))) {
                        final.ES.result <- rbind(final.ES.result,
                                                    c(ES.result[i, -c(3:9)],
                                                    ES.mat.2[j, 3],
                                                    ES.result[i, 4],
                                                    ES.result[i, -c(3:9)],
                                                    ES.mat.2[j, 7],
                                                    ES.result[i, 8],
                                                    ES.result[i, 9]))
                        final.ES.result <- rbind(final.ES.result,
                                                    c(ES.result[i, -c(4:9)],
                                                    ES.mat.2[j, 4],
                                                    ES.result[i, 5:7],
                                                    ES.mat.2[j, 8],
                                                    ES.result[i, 9]))
                    }
                }
            }
            ES.result <- unique(rbind(ES.result, final.ES.result, ES.mat.2))
            ES.result
        }
    }
    inclu.flack.ex <- lapply(paste(final.SE.EX[, "txid"],
                                    final.SE.EX[, "start"],
                                    final.SE.EX[, "end"], sep = "-"),
                                    get.inclu.flack.ex)
    ES.mat <- do.call(rbind, inclu.flack.ex)
    if (length(ES.mat) == 0) {
        return(NULL)
    }
    ES.mat <- unique(ES.mat)
    sec.mxe.mat <- rbind(ES.mat[ES.mat[, 2] != "NA", ])
    u.1st.ex <- unique(ES.mat[ES.mat[, 2] == "NA", 1])
    u.do.ex <- unique(ES.mat[ES.mat[, 2] == "NA", 3])
    u.up.ex <- unique(ES.mat[ES.mat[, 2] == "NA", 4])
    final.pre.ES.mat <- NULL
    for (i in seq_len(length(u.1st.ex))) {
        for (j in seq_len(length(u.do.ex))) {
            if (u.1st.ex[i] == u.do.ex[j]) {
                next
            }
            do.des <- unique(ES.mat[ES.mat[, 3] == u.do.ex[j], 7])
            pre.ES.mat <- do.call(rbind, lapply(u.up.ex, function(each.up.ex) {
                if (u.1st.ex[i] != each.up.ex) {
                    up.des <- unique(ES.mat[ES.mat[, 4] == each.up.ex, 8])
                    cbind(u.1st.ex[i], "NA", u.do.ex[j], each.up.ex,
                            u.1st.ex[i],
                            "NA", do.des, up.des, "SE")
                }
            }))
            final.pre.ES.mat <- rbind(final.pre.ES.mat, pre.ES.mat)
        }
    }
    ES.mat <- unique(rbind(final.pre.ES.mat, sec.mxe.mat))
    colnames(ES.mat) <- c("TarEX", "2ndEX", "DownEX", "UpEX", "Tar_des",
                            "2nd_des", "Do_des", "Up_des", "Types")
    final.MXE.cal <- NULL
    pre.MXE.mat <- NULL
    MXE.ES.mat <- NULL
    final.down.ex <- unique(do.call(rbind, strsplit(ES.mat[, "DownEX"], "-")))
    final.up.ex <- unique(do.call(rbind, strsplit(ES.mat[, "UpEX"], "-")))
    colnames(final.down.ex) <- c("start", "end")
    colnames(final.up.ex) <- c("start", "end")
    u.final.SE.EX <- cbind("1", rbind(unique(final.SE.EX[, c("start", "end")])))
    colnames(u.final.SE.EX) <- c("txid", "start", "end")
    get.final.MXE.cal <- function(total.es) {
        MXE.mat <- NULL
        each.es <- as.double(strsplit(total.es, "-")[[1]])
        names(each.es) <- c("txid", "start", "end")
        pre.SE.intron <- rbind(ES.mat[is.element(ES.mat[, "TarEX"],
                                paste(each.es["start"], each.es["end"],
                                        sep = "-")), ])
        if (length(pre.SE.intron) != 0) {
            SE.intron <- cbind(do.call(rbind,
                                strsplit(pre.SE.intron[, "DownEX"], "-"))[, 2],
                                do.call(rbind,
                                strsplit(pre.SE.intron[, "TarEX"], "-"))[, 1])
            SE.intron <- rbind(SE.intron, cbind(do.call(rbind,
                                strsplit(pre.SE.intron[, "TarEX"], "-"))[, 2],
                                do.call(rbind,
                                strsplit(pre.SE.intron[, "UpEX"], "-"))[, 1]))
            u.SE.intron <- rbind(unique(SE.intron))
            get.MXE.ex.test <- function(mxe.intron) {
                mxe.intron <- as.integer(unlist(strsplit(mxe.intron, "-")))
                do.mxe <- final.down.ex[as.integer(final.down.ex[, "start"]) >
                                        mxe.intron[1] - 1 &
                                        as.integer(final.down.ex[, "end"]) <
                                        mxe.intron[2] + 1, ]
                up.mxe <- final.up.ex[as.integer(final.up.ex[, "start"]) >
                                        mxe.intron[1] - 1 &
                                        as.integer(final.up.ex[, "end"]) <
                                        mxe.intron[2] + 1, ]
                rbind(do.mxe, up.mxe)
            }
            MXE.ex.test <- lapply(paste(u.SE.intron[, 1], u.SE.intron[, 2],
                                        sep = "-"), get.MXE.ex.test)
            MXE.ex.test <- do.call(rbind, MXE.ex.test)
            if (length(MXE.ex.test) != 0) {
                MXE.ex.test <- unique(rbind(MXE.ex.test))
                get.MXE.mat <- function(total.other.ex) {
                other.ex <- unlist(strsplit(total.other.ex, "-"))
                if (as.double(each.es["end"]) < as.double(other.ex[1])) {
                    MXE.cal <- cbind(paste(each.es[-1], collapse = "-"),
                                        paste(other.ex, collapse = "-"))
                } else if (as.double(each.es["start"]) >
                            as.double(other.ex[2])) {
                    MXE.cal <- cbind(paste(other.ex, collapse = "-"),
                                        paste(each.es[-1], collapse = "-"))
                    }
                }
                MXE.mat <- do.call(rbind, lapply(paste(MXE.ex.test[, 1],
                                    MXE.ex.test[, 2], sep = "-"), get.MXE.mat))
            }
        }
        MXE.mat
    }
    final.MXE.cal <- do.call(rbind, lapply(paste(u.final.SE.EX[, 1],
                                                    u.final.SE.EX[, 2],
                                                    u.final.SE.EX[, 3],
                                                    sep = "-"),
                                get.final.MXE.cal))
    if (length(final.MXE.cal) != 0) {
        MXE.cal <- final.MXE.cal
        MXE.cal <- unique(MXE.cal)
        if (length(MXE.cal) != 0) {
            get.MXE.ES.mat <- function(total.mem) {
                mem <- strsplit(total.mem, "-")[[1]]
                ES.do <- do.call(rbind, strsplit(ES.mat[, "DownEX"], "-"))
                ES.up <- do.call(rbind, strsplit(ES.mat[, "UpEX"], "-"))
                MXE.ES <- unique(rbind(ES.mat[as.double(ES.do[, 1]) <
                                    min(as.double(mem)) &
                                    as.double(ES.up[, 2]) >
                                    max(as.double(mem)),
                                    c("DownEX", "UpEX", "Do_des",
                                        "Up_des", "Types")]))
                if (length(MXE.ES) != 0) {
                    tar.exs <- matrix(rep(c(paste(mem[seq_len(2)],
                                        collapse = "-"),
                                        paste(mem[3:4], collapse = "-")),
                                        nrow(MXE.ES)), nrow = nrow(MXE.ES),
                                        byrow = TRUE)
                    cbind(tar.exs, rbind(MXE.ES[, c("DownEX", "UpEX")]),
                            tar.exs, rbind(MXE.ES[, c("Do_des", "Up_des",
                                                        "Types")]))
                }
            }
            MXE.ES.mat <- do.call(rbind, lapply(paste(MXE.cal[, 1],
                                    MXE.cal[, 2], sep = "-"), get.MXE.ES.mat))
            if (length(MXE.ES.mat) != 0) {
                colnames(MXE.ES.mat) <- c("1stEX", "2ndEX", "DownEX", "UpEX",
                                            "1st_des", "2nd_des", "Do_des",
                                            "Up_des", "Types")
                MXE.ES.mat[, "Types"] <- "MXE"
            }
        }
        ES.mat <- rbind(ES.mat, unique(MXE.ES.mat))
    }
    ES.mat <- unique(ES.mat)
    down.ex.e <- as.double(do.call(rbind,
                                    strsplit(ES.mat[, "DownEX"], "-"))[, 2])
    fi.ex.s.e <- do.call(rbind, strsplit(ES.mat[, "TarEX"], "-"))
    up.ex.e <- as.double(do.call(rbind, strsplit(ES.mat[, "UpEX"], "-"))[, 1])
    ES.mat <- rbind(ES.mat[down.ex.e < as.double(fi.ex.s.e[, 1]) &
                        as.double(fi.ex.s.e[, 2]) < up.ex.e, ])
    ES.mat <- cbind(ES.mat, "possible")
    colnames(ES.mat) <- c("1stEX", "2ndEX", "DownEX", "UpEX", "1st_des",
                            "2nd_des", "Do_des", "Up_des", "Types", "status")
    po.test.mat <- paste(do.call(rbind, strsplit(ES.mat[, "DownEX"], "-"))[, 2],
                            do.call(rbind,
                                strsplit(ES.mat[, "1stEX"], "-"))[, 1],
                            sep = "-")
    po.test.mat <- cbind(po.test.mat,
                            paste(do.call(rbind,
                            strsplit(ES.mat[, "1stEX"], "-"))[, 2],
                            do.call(rbind,
                            strsplit(ES.mat[, "UpEX"], "-"))[, 1], sep = "-"))
    po.test.mat <- cbind(po.test.mat, paste(do.call(rbind,
                            strsplit(ES.mat[, "DownEX"], "-"))[, 2],
                            do.call(rbind,
                            strsplit(ES.mat[, "UpEX"], "-"))[, 1], sep = "-"))
    po.test.mat <- cbind(po.test.mat, rbind(ES.mat[, 3:4]))
    intron.info.mat <- paste(intron.info[, "start"] - 1,
                                intron.info[, "end"] + 1, sep = "-")
    names(intron.info.mat) <- rownames(intron.info)
    exon.info.mat <- paste(exon.info[, "start"], exon.info[, "end"], sep = "-")
    names(exon.info.mat) <- rownames(exon.info)
    po.over.result <- lapply(seq_len(nrow(po.test.mat)),
                                function(total.ptm.num) {
        ptm <- po.test.mat[total.ptm.num, ]
        ptm.test.int <- which(is.element(
                                names(intron.info.mat)[which(intron.info.mat ==
                                                                    ptm[1])],
                                names(intron.info.mat)[which(intron.info.mat ==
                                                                    ptm[2])]) ==
                                    "TRUE")
        ptm.test.ex <- intersect(names(exon.info.mat)[which(exon.info.mat ==
                                                                    ptm[4])],
                                    names(exon.info.mat)[which(exon.info.mat ==
                                                                    ptm[5])])
        ptm.test.ski.int <- names(intron.info.mat)[which(intron.info.mat ==
                                                                    ptm[3])]
        if (length(intersect(ptm.test.ex, ptm.test.ski.int)) != 0 &
            length(ptm.test.int) != 0) {
            total.ptm.num
        }
    })
    po.over.result <- is.element(seq_len(nrow(ES.mat)), unlist(po.over.result))
    po.over.result <- po.over.result & (ES.mat[, "2ndEX"] == "NA")
    ES.mat[po.over.result, "status"] <- "exist"
    se.exons.num <- ES.mat[, "2ndEX"] != "NA" & ES.mat[, "Types"] == "SE"
    se.MXE.num <- ES.mat[, "2ndEX"] != "NA" & ES.mat[, "Types"] == "MXE"
    if (length(which(se.exons.num == "TRUE")) != 0) {
        es.se.test <- NULL
        es.se.ex <- rbind(ES.mat[se.exons.num, ])
        for (i in seq_len(nrow(es.se.ex))) {
            es.se.1 <- which(is.element(names(exon.info.mat)[which(
                                exon.info.mat == es.se.ex[i, 1])],
                                names(exon.info.mat)[which(
                                exon.info.mat == es.se.ex[i, 2])])
                                == "TRUE")
            es.se.2 <- which(intron.info.mat ==
                                paste(unlist(strsplit(es.se.ex[i, 3], "-"))[2],
                                unlist(strsplit(es.se.ex[i, 4], "-"))[1],
                                sep = "-"))
            if (length(es.se.1) != 0 & length(es.se.2) != 0) {
                es.se.test <- c(es.se.test, 1 == 1)
            }
        }
        ES.mat[which(se.exons.num == "TRUE")[es.se.test], "status"] <- "exist"
    }
    if (length(which(se.MXE.num == "TRUE")) != 0) {
        mxe.se <- rbind(ES.mat[se.MXE.num, ])
        mxe.se.1 <- paste(do.call(rbind,
                            strsplit(mxe.se[, "1stEX"], "-"))[, 2],
                            do.call(rbind,
                            strsplit(mxe.se[, "UpEX"], "-"))[, 1],
                            sep = "-")
        mxe.se.2 <- paste(do.call(rbind,
                            strsplit(mxe.se[, "DownEX"], "-"))[, 2],
                            do.call(rbind,
                            strsplit(mxe.se[, "2ndEX"], "-"))[, 1], sep = "-")
        mxe.se.3 <- paste(do.call(rbind,
                            strsplit(mxe.se[, "DownEX"], "-"))[, 2],
                            do.call(rbind,
                            strsplit(mxe.se[, "1stEX"], "-"))[, 1], sep = "-")
        mxe.se.4 <- paste(do.call(rbind, strsplit(mxe.se[, "2ndEX"], "-"))[, 2],
                            do.call(rbind,
                            strsplit(mxe.se[, "UpEX"], "-"))[, 1], sep = "-")
        mxe.se.test <- is.element(mxe.se.1, intron.info.mat) &
                        is.element(mxe.se.2, intron.info.mat) &
                        is.element(mxe.se.3, intron.info.mat) &
                        is.element(mxe.se.4, intron.info.mat)
        ES.mat[which(se.MXE.num == "TRUE")[mxe.se.test], "status"] <- "exist"
    }
    rownames(ES.mat) <- seq_len(nrow(ES.mat))
    colnames(ES.mat) <- c("1stEX", "2ndEX", "DownEX", "UpEX", "1st_des",
                            "2nd_des", "Do_des", "Up_des", "Types", "status")
    ES.mat <- rbind(ES.mat[, c("1stEX", "2ndEX", "DownEX", "UpEX", "Types",
                                "status")])
    return(unique(ES.mat))
}