R/all_generics.R

In rmflight/categoryCompare2: Meta-Analysis of High-Throughput Experiments Using Feature Annotations

#' 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")
  }
)