R/makeGRangesListFromEvent.R

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

#' Make a GRangesList object from an AS event
#'
#' This function makes a GRangesList object from an AS event.
#'
#' @param event AS event ID in ASpedia format
#' @return a GRangesList object
#' @keywords internal
#' @importFrom GenomicRanges makeGRangesListFromDataFrame
#' @noRd
makeGRangesListFromEvent <- function(event, gtf) {
    event <- unlist(strsplit(event, split = ":"))
    genesymbol <- event[1]
    geneid <- gtf$gene_id[grep(genesymbol, gtf$gene_name)[1]]
    type <- event[2]
    seqname <- event[3]
    strand <- ifelse(as.numeric(event[4]) < as.numeric(event[length(event)]),
                        "+", "-")
    coords <- as.numeric(event[4:length(event)])

    if (strand == "-") {
        coords <- rev(coords)
    }

    if ((type == "A5SS" & strand == "+") | (type == "A3SS" & strand == "-")) {
        df <- data.frame(seqname = seqname, start = coords[c(1, 1, 4)],
                            end = coords[c(2, 3, 5)], strand = strand,
                            exon = c("exon_short", "exon_long",
                                        "exon_flanking"),
                            GeneID = geneid, geneSymbol = genesymbol,
                            stringsAsFactors = FALSE)
        grl <- makeGRangesListFromDataFrame(df, split.field = "exon",
                                                keep.extra.columns = TRUE)
        grl <- grl[c("exon_long", "exon_short", "exon_flanking")]
    }

    if ((type == "A3SS" & strand == "+") | (type == "A5SS" & strand == "-")) {
        df <- data.frame(seqname = seqname, start = coords[c(1, 3, 4)],
                            end = coords[c(2, 5, 5)], strand = strand,
                            exon = c("exon_flanking", "exon_long",
                                        "exon_short"), GeneID = geneid,
                            geneSymbol = genesymbol, stringsAsFactors = FALSE)
        grl <- makeGRangesListFromDataFrame(df, split.field = "exon",
                                                keep.extra.columns = TRUE)
        grl <- grl[c("exon_long", "exon_short", "exon_flanking")]
    }

    if (type == "SE") {
        df <- data.frame(seqname = seqname, start = coords[c(3, 1, 5)],
                            end = coords[c(4, 2, 6)], strand = strand,
                            exon = c("exon_target", "exon_upstream",
                                        "exon_downstream"), GeneID = geneid,
                            geneSymbol = genesymbol, stringsAsFactors = FALSE)
        grl <- makeGRangesListFromDataFrame(df, split.field = "exon",
                                                keep.extra.columns = TRUE)
        grl <- grl[c("exon_target", "exon_upstream", "exon_downstream")]
    }

    if (type == "MXE") {
        df <- data.frame(seqname = seqname, start = coords[c(1, 3, 5, 7)],
                            end = coords[c(2, 4, 6, 8)], strand = strand,
                            exon = c("exon_upstream", "exon_1", "exon_2",
                                        "exon_downstream"), GeneID = geneid,
                            geneSymbol = genesymbol, stringsAsFactors = FALSE)
        grl <- makeGRangesListFromDataFrame(df, split.field = "exon",
                                                keep.extra.columns = TRUE)
        grl <- grl[c("exon_1", "exon_2", "exon_upstream", "exon_downstream")]
    }

    if (type == "RI") {
        df <- data.frame(seqname = seqname, start = coords[c(1, 1, 3)],
                            end = coords[c(4, 2, 4)], strand = strand,
                            exon = c("exon_ir", "exon_upstream",
                                        "exon_downstream"), GeneID = geneid,
                            geneSymbol = genesymbol, stringsAsFactors = FALSE)
        grl <- makeGRangesListFromDataFrame(df, split.field = "exon",
                                                keep.extra.columns = TRUE)
        grl <- grl[c("exon_ir", "exon_upstream", "exon_downstream")]
    }

    return(list(grl = grl, type = type))
}