R/EnsemblGenes.R

In acidgenomics/AcidGenomes: Acid Genomics Genome Annotations

#' Generate an `EnsemblGenes` object
#'
#' @export
#' @note Updated 2023-04-26.
#'
#' @param object `GRanges`.
#' Must contain Ensembl annotations previously generated by
#' `makeGRangesFromEnsembl` or `makeGRangesFromGff`.
#'
#' @examples
#' ## > object <- makeGRangesFromEnsembl("Homo sapiens")
#' ## > object <- as(object, "GRanges")
#' ## > object <- EnsemblGenes(object)
#' ## > print(object)
EnsemblGenes <- # nolint
    function(object) {
        if (is(object, "EnsemblGenes")) {
            assert(validObject(object))
            return(object)
        }
        assert(
            is(object, "GRanges"),
            hasNames(mcols(object))
        )
        names(mcols(object)) <- camelCase(names(mcols(object)), strict = TRUE)
        assert(isSubset("geneId", names(mcols(object))))
        if (any(grepl("^transcript", names(mcols(object))))) {
            names(mcols(object)) <- sub(
                pattern = "^transcript",
                replacement = "tx",
                x = names(mcols(object))
            )
        }
        if (isSubset("entrezId", names(mcols(object)))) {
            names(mcols(object))[
                names(mcols(object)) == "entrezId"
            ] <- "ncbiGeneId"
        }
        meta <- metadata(object)
        if (is.null(meta[["date"]])) {
            meta[["date"]] <- Sys.Date()
        }
        if (is.null(meta[["ignoreVersion"]])) {
            meta[["ignoreVersion"]] <-
                !isSubset("geneIdNoVersion", names(mcols(object)))
        }
        if (is.null(meta[["level"]])) {
            meta[["level"]] <- ifelse(
                test = isTRUE(isSubset("txId", names(mcols(object)))),
                yes = "transcripts",
                no = "genes"
            )
        }
        if (is.null(meta[["organism"]])) {
            meta[["organism"]] <-
                detectOrganism(as.character(mcols(object)[["geneId"]]))
        }
        if (is.null(meta[["packageVersion"]])) {
            meta[["packageVersion"]] <- .pkgVersion
        }
        if (is.null(meta[["provider"]])) {
            meta[["provider"]] <- "Ensembl"
        }
        assert(identical(meta[["provider"]], "Ensembl"))
        metadata(object) <- meta
        new(Class = "EnsemblGenes", object)
    }