R/get_info.R

In kbroman/GNapi: Connection to the GeneNetwork API

#' Get summary information about a phenotype
#'
#' Get summary information about a phenotype
#'
#' @param group Name of a group of datasets
#' @param trait Trait identifier (can be a vector)
#' @param url The URL for the GeneNetwork API
#'
#' @return A data frame
#'
#' @export
#'
#' @examples
#' info_pheno("BXD", "10002")
#' info_pheno("HC_M2_0606_P", "1436869_at")
info_pheno <-
    function(group, trait, url=gnapi_url())
{
    stopifnot(length(group)==1)
    if(is.null(trait) || (length(trait)==1 && trait == "")) {
        stop("trait must be provided; can be a vector")
    }

    if(length(trait) > 1) {
        result <- lapply(trait, function(trt) info_pheno(group, trait=trt, url=url))
        return(do.call("rbind_expand", result))
    }

    result <- query_gn(paste0("trait/", group, "/", trait), url=url)

    if(is.null(result)) return(result)

    # convert to a data frame
    result <- list2df(list(result))
    rownames(result) <- trait

    result
}