R/getGenome.R

In DessimozLab/OmaDB: R wrapper for the OMA REST API

#' Retrieve a genome from the OMA Browser database
#'
#' This function obtains the basic information for one specific genome available
#' on the OMA Browser, or - if no id is provided - a dataframe with all available
#' genomes.
#'
#' Ids can be either the scientific name of a species, the NCBI taxonomy id or
#' the UniProtKB mnemonic species code.
#'
#' The optional argument attribute can be used to directly load the proteins
#' belonging to the genome. Alternatively, you can access the proteins attribute
#' of the result which will transparently load the proteins from the OMA Browser.
#'
#' @param id A genome identifier. By default, all available genomes will be returned.
#' @param attribute An extra attribute to be returned (proteins)
#' @return an object containing the JSON keys as attributes or a dataframe
#' @export
#' @examples
#' getGenome()
#' getGenome(id='HUMAN')
#' getGenome(id=9606)
#' getGenome(id='YEAST',attribute='proteins')

getGenome <- function(id = NULL, attribute = NULL) {

    if (!is.null(attribute) && !(attribute %in% c("proteins"))) {
        stop("You must provide a valid attribute.")
    }

    url <- urlGenerator(endpoint = "genome", id = id, detail = attribute)

    return(requestFactory(url))
}