R/makeProteinToGene.R

In acidgenomics/AcidGenomes: Acid Genomics Genome Annotations

#' Map protein identifiers to genes
#'
#' @name makeProteinToGene
#' @note Updated 2023-09-16.
#'
#' @inheritParams AcidRoxygen::params
#' @param ids `character`.
#' Ensembl protein identifiers.
#' Human proteins are prefixed with "ENSP", for example.
#'
#' @return `ProteinToGene`.
#'
#' @examples
#' ids <- c("ENSP00000238714", "ENSP00000338157")
#' object <- makeProteinToGeneFromEnsembl(ids)
#' print(object)
NULL



#' @rdname makeProteinToGene
#' @export
makeProteinToGeneFromEnsembl <-
    function(ids,
             organism = NULL,
             genomeBuild = NULL,
             release = NULL) {
        assert(
            requireNamespaces("ensembldb"),
            isCharacter(ids),
            hasNoDuplicates(ids)
        )
        alert(sprintf("Making {.cls %s} from Ensembl.", "ProteinToGene"))
        if (is.null(organism)) {
            organism <- detectOrganism(ids)
        }
        edb <- .getEnsDb(
            organism = organism,
            genomeBuild = genomeBuild,
            release = release
        )
        ## The `select()` generic is defined in AnnotationDbi.
        quietly({
            df <- ensembldb::select(
                x = edb,
                keys = ids,
                keytype = "PROTEINID",
                columns = c("GENEID", "GENENAME")
            )
        })
        df <- as(df, "DFrame")
        colnames(df) <- tolower(colnames(df))
        colnames(df) <- gsub("id$", "Id", colnames(df))
        colnames(df) <- gsub("name$", "Name", colnames(df))
        if (!areSetEqual(ids, unique(df[["proteinId"]]))) {
            abort(sprintf(
                "Match failure: %s.",
                toInlineString(
                    sort(setdiff(ids, unique(df[["proteinId"]]))),
                    n = 10L
                )
            ))
        }
        meta <- .getEnsDbMetadata(edb)
        meta[["date"]] <- Sys.Date()
        meta[["packageVersion"]] <- .pkgVersion
        meta <- meta[sort(names(meta))]
        metadata(df) <- meta
        new(Class = "ProteinToGene", df)
    }