#' @name geneSet
#' @inherit AcidGenerics::geneSet
#' @note Updated 2022-04-27.
#' @inheritParams params
#' @param ... Additional arguments.
#' @examples
#' data(fgsea)
#'
#' ## FgseaList ====
#' object <- fgsea
#' collection <- collectionNames(object)[[1L]]
#' set <- geneSetNames(object = object, collection = collection)[[1L]]
#' x <- geneSet(
#' object = object,
#' collection = collection,
#' set = set
#' )
#' head(x)
NULL
## Updated 2020-09-21.
`geneSet,FgseaList` <- # nolint
function(object,
collection,
set) {
validObject(object)
assert(
isString(collection),
isSubset(collection, collectionNames(object)),
isString(set)
)
x <- metadata(object)[["collections"]][[collection]][[set]]
assert(isCharacter(x))
x
}
#' @rdname geneSet
#' @export
setMethod(
f = "geneSet",
signature = signature(object = "FgseaList"),
definition = `geneSet,FgseaList`
)
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