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#' @title Retrieve available kingdoms of life
#' @description A short list of available kingdoms of life
#' @param db a character string specifying the database from which the genome
#' shall be retrieved: \code{db = "refseq"}, \code{db = "genbank"},
#' \code{db = "ensembl"}, \code{db = "ensemblgenomes"}.
#' Default is \code{db = "refseq"}.
#' @author Hajk-Georg Drost
#' @examples
#' # retrieve kingdoms available from refseq
#' getKingdoms(db = "refseq")
#'
#' # retrieve kingdoms available from genbank
#' getKingdoms(db = "genbank")
#' @seealso \code{\link{meta.retrieval}}, \code{\link{getGenome}},
#' \code{\link{getProteome}}, \code{\link{getCDS}}, \code{\link{getGroups}}
#' @export
getKingdoms <- function(db = "refseq") {
withr::local_options(timeout = max(30000000, getOption("timeout")))
if (!is.element(db, c("refseq", "genbank", "ensembl", "ensemblgenomes")))
stop("Please select one of the available data bases: 'refseq',
'genbank', 'ensembl', or 'ensemblgenomes'.", call. = FALSE)
if (db == "refseq") {
return(getKingdomRefseq())
}
if (db == "genbank") {
return(getKingdomGenbank())
}
if (db %in% c("ensembl", "ensemblgenomes")) {
return(getKingdomEnsembl())
}
}
getKingdomGenbank <- function() {
c(
"archaea",
"bacteria",
"fungi",
"invertebrate",
"plant",
"protozoa",
"vertebrate_mammalian",
"vertebrate_other"
)
}
getKingdomRefseq <- function() {
c(getKingdomGenbank(), "viral")
}
getKingdomEnsembl <- function() {
ensembl_divisions_short()
}
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