R/createExonTable.R

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

#' Create an exon table
#'
#' This function creates an exon table
#'
#' @param gtf_exons A GRanges object containing exons in gtf
#' @param ids transcript ids
#' @return a data frame containing an exon table
#' @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 dplyr filter
#' @noRd
createExonTable <- function(gtf_exons, ids) {
    transcript_id <- NULL
    res <- filter(as.data.frame(gtf_exons), transcript_id %in% ids)
    res.df <- res[, c("seqnames", "start", "end", "strand", "exon_id",
                        "transcript_name")]
    colnames(res.df) <- c("chromosome", "start", "end", "strand", "exon",
                            "transcript")
    return(res.df)
}