Query DisGeNET disease / gene database from R

DisGeNET.R

#' Query DisGeNET disease / gene database
#'
#' Based on a script by [email protected], retrieved from
#' http://www.disgenet.org/ds/DisGeNET/scripts/disgenet.R on 7 April,
#' 2016. This version is meant for interactive use within an R
#' session, and makes a single query to DisGeNET rather than one query
#' for each input symbol.
#' 
#' @param input: character vector of gene or disease identifiers
#'
#' @param entity: character(1) specifying that the identifiers are
#'     either "gene" or "disease"
#'
#' @param identifier: character(1) specifying the type of
#'     identifier. If 'entity' is "gene", then 'identifier' can be
#'     "entrez", or "hgnc". If 'entity' is "disease", 'identifier' can
#'     be 'cui', 'mesh', or 'omim'.
#'
#' @examples
#' input <- c("CDK1", "CDK1A", "CDK2")
#' result <- DisGeNET(input, 'gene', 'hgnc')
#' head(result)
#' 
DisGeNET <- function(input, entity = c("gene", "disease"), identifier) {
    loadNamespace("httr")

    stopifnot(is.character(input))
    entity <- match.arg(entity)
    stopifnot(is.character(identifier), length(identifier) == 1L)

    STR <- switch(entity, gene={
        if (!identifier %in% c("entrez", "hgnc"))
            stop("entity='gene' 'identifier' must be 'entrez' or 'hgnc'")
        if (identifier == "entrez")
            "c2.geneId"
        else                            # identifier = 'hgnc'
            "c2.name"
    }, disease={
        if (!identifier %in% c("cui", "mesh", "omim"))
            stop("entity='disease' 'identifier' must be 'cui', 'mesh' or 'omim'")
        paste0("c1.", identifier)
    })
                  
    url <- "http://www.disgenet.org/oql"
    terms <- paste(sprintf("'%s'", input), collapse=", ")

    oql <- paste0(
        "DEFINE
            c0='/data/gene_disease_score_onexus',
            c1='/data/diseases',
            c2='/data/genes',
            c3='/data/sources'
        ON
            'http://bitbucket.org/janis_pi/disgenet_onexus.git'
        SELECT
            c1 (cui, name, diseaseClassName, STY, MESH, omimInt),
            c2 (geneId, name, uniprotId, description, pathName, pantherName),
            c0 (score, pmids)
        FROM
            c0
        WHERE
            (c3 = 'ALL' AND ", STR, " IN (",  terms, ")
        ORDER BY ",
            STR, ", c0.score DESC")

    response <- httr::POST(url, body=oql)
    httr::stop_for_status(response)
    tbl <- read.csv(text=httr::content(response), header=TRUE, sep="\t")

    bad <- !input %in% tbl$c2.name
    if (any(bad))
        warning("entitites not in DisGeNET:\n  ",
                paste(sQuote(input[bad]), collapse=", "),
                call.=FALSE)

    tbl
}