R/internal-annotationhub.R

In acidgenomics/AcidGenomes: Acid Genomics Genome Annotations

#' Connect to AnnotationHub
#'
#' @note Updated 2023-04-26.
#' @noRd
#'
#' @details
#' On a fresh install this will print a txProgressBar to the console. We're
#' using `capture.output()` here to suppress the console output, since it's not
#' very informative and can cluster R Markdown reports.
.annotationHub <- function() {
    assert(
        requireNamespaces("AnnotationHub"),
        hasInternet()
    )
    quietly({
        ah <- AnnotationHub::AnnotationHub(ask = FALSE)
    })
    assert(is(ah, "AnnotationHub"))
    ah
}



#' Get Ensembl / NCBI (Entrez) mappings from NCBI OrgDb via AnnotationHub
#'
#' @note Updated 2023-11-27.
#' @noRd
.getEnsemblToNcbiFromOrgDb <-
    function(keys, organism, return) {
        assert(
            requireNamespaces(c("AnnotationDbi", "AnnotationHub")),
            isCharacter(keys),
            hasNoDuplicates(keys),
            isOrganism(organism)
        )
        return <- match.arg(
            arg = return,
            choices = c("EnsemblToNcbi", "NcbiToEnsembl")
        )
        switch(
            EXPR = return,
            "EnsemblToNcbi" = {
                keytype <- "ENSEMBL"
                columns <- "ENTREZID"
            },
            "NcbiToEnsembl" = {
                keytype <- "ENTREZID"
                columns <- "ENSEMBL"
            }
        )
        alert(sprintf(
            "Matching %d %s using NCBI {.cls %s} via {.pkg %s} %s.",
            length(keys),
            ngettext(
                n = length(keys),
                msg1 = "identifier",
                msg2 = "identifiers"
            ),
            "OrgDb", "AnnotationHub",
            packageVersion("AnnotationHub")
        ))
        ah <- .annotationHub()
        ahs <- AnnotationHub::query(
            x = ah,
            pattern = c(organism, "NCBI", "OrgDb")
        )
        id <- tail(names(ahs), n = 1L)
        quietly({
            orgdb <- ah[[id]]
        })
        assert(is(orgdb, "OrgDb"))
        alertInfo(sprintf(
            "{.val %s} (%s): %s.",
            id,
            mcols(ahs)[id, "title"],
            mcols(ahs)[id, "description"]
        ))
        quietly({
            df <- AnnotationDbi::select(
                x = orgdb,
                keys = keys,
                keytype = keytype,
                columns = columns
            )
        })
        assert(
            is.data.frame(df),
            identical(keys, unique(df[[keytype]]))
        )
        i <- complete.cases(df)
        df <- df[i, , drop = FALSE]
        if (!areSetEqual(keys, unique(df[[keytype]]))) {
            setdiff <- setdiff(keys, unique(df[[keytype]]))
            abort(sprintf(
                "%d match %s: %s.",
                length(setdiff),
                ngettext(
                    n = length(setdiff),
                    msg1 = "failure",
                    msg2 = "failures"
                ),
                toInlineString(setdiff, n = 10L)
            ))
        }
        colnames(df)[colnames(df) == "ENSEMBL"] <- "ensemblGeneId"
        colnames(df)[colnames(df) == "ENTREZID"] <- "ncbiGeneId"
        df[["ncbiGeneId"]] <- as.integer(df[["ncbiGeneId"]])
        df <- as(df, "DFrame")
        rownames(df) <- as.character(df[[1L]])
        metadata(df)[["organism"]] <- organism
        df
    }