#' combine enrichments
#'
#' @export
setGeneric("combine_enrichments", function(...) {
standardGeneric("combine_enrichments")
})
#' combine annotations
#'
#' @export
setGeneric("combine_annotations", function(annotation_list) {
standardGeneric("combine_annotations")
})
#' get significant annotations
#'
#' @export
setGeneric("get_significant_annotations", function(in_results, ...) {
standardGeneric("get_significant_annotations")
})
#' get statistics
#'
#' @export
setGeneric("extract_statistics", function(in_results) {
standardGeneric("extract_statistics")
})
#' generate annotation graph
#'
#' @export
setGeneric(
"generate_annotation_graph",
function(
comb_enrichment,
annotation_similarity = "combined",
low_cut = 5,
hi_cut = 500
) {
standardGeneric("generate_annotation_graph")
}
)
#' generate statistical table
#'
#' @export
setGeneric(
"generate_table",
function(comb_enrichment, entries = "signficant", link_type = "explicit") {
standardGeneric("generate_table")
}
)
#' unique annotation combinations
#'
#' @export
setGeneric("annotation_combinations", function(object) {
standardGeneric("annotation_combinations")
})
# we may unexport this eventually
#' remove edges
#'
#' @export
setGeneric(
"remove_edges",
function(edge_obj, cutoff, edge_attr = "weight", value_direction = "under") {
standardGeneric("remove_edges")
}
)
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