#' @describeIn as.GeneSetCollection Convert a list to a GeneSetCollection object
#' @export as.GeneSetCollection
setMethod("as.GeneSetCollection", signature(object = "list"),
function(object, ...){
keep <- vapply(object, function(x){
all(is(x, "character"))
}, FUN.VALUE = logical(1))
object <- object[keep]
paths2gene <- inverseList(object)
paths2gene <- lapply(paths2gene, unique)
gsl <- sapply(names(paths2gene), function(x){
GeneSet(paths2gene[[x]], setName = x)})
check(GeneSetCollection(gsl))
}
)
#' @describeIn as.GeneSetCollection Convert AnnDbBimap to GeneSetCollections
#' @export as.GeneSetCollection
setMethod("as.GeneSetCollection",
signature(object = "AnnDbBimap"),
function(object, ...) {
check(as.GeneSetCollection(as.list(object), ...))
}
)
setAs("list", "GeneSetCollection",
function(from) { as.GeneSetCollection(from)}
)
setAs("AnnDbBimap", "GeneSetCollection",
function(from) { as.GeneSetCollection(from)}
)
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