adds constructors for the 3 main enrichment types used

Author: rmflight

NAMESPACE

@@ -8,6 +8,7 @@ export(assign_colors)
 export(assign_communities)
 export(binomial_basic)
 export(binomial_feature_enrichment)
+export(binomial_features)
 export(cc_graph)
 export(combine_annotation_features)
 export(combine_annotations)
@@ -35,9 +36,11 @@ export(get_significant_annotations_calls)
 export(gocats_to_annotation)
 export(graph_to_visnetwork)
 export(gsea_feature_enrichment)
+export(gsea_features)
 export(gsea_result_to_fgsea)
 export(hypergeometric_basic)
 export(hypergeometric_feature_enrichment)
+export(hypergeometric_features)
 export(hypergeometric_result)
 export(install_executables)
 export(jaccard_coefficient)

R/binomial_enrichment.R

@@ -16,6 +16,25 @@ setClass(
   )
 )
 
+#' binomial_features constructor
+#'
+#' Create the binomial_features-class object.
+#'
+#' @param positivefc the positively changed features
+#' @param negativefc the negatively changed features
+#' @param annotation the annotation object
+#'
+#' @export
+#' @return binomial_features-class
+binomial_features = function(positivefc, negativefc, annotation) {
+  new(
+    "binomial_features",
+    positivefc = positivefc,
+    negativefc = negativefc,
+    annotation = annotation
+  )
+}
+
 #' do binomial testing
 #'
 #' @param binomial_features a binomial_features object

R/gsea.R

@@ -11,6 +11,19 @@ setClass(
   slots = list(ranks = "ANY", annotation = "annotation")
 )
 
+#' gsea_features constructor
+#'
+#' Creates a gsea_features-class object.
+#'
+#' @param ranks a named vector of ranks
+#' @param annotation the annotation object
+#'
+#' @export
+#' @return gsea_features-class
+gsea_features = function(ranks, annotation) {
+  new("gsea_features", ranks = ranks, annotation = annotation)
+}
+
 #' do GSEA
 #'
 #' Performs gene-set enrichment analysis using the `fgsea` package.

R/hypergeometric_enrichment.R

@@ -12,6 +12,25 @@ setClass(
   slots = list(significant = "ANY", universe = "ANY", annotation = "annotation")
 )
 
+#' hypergeometric_features constructor
+#'
+#' function to easily construct a hypergeometric_features-class object.
+#'
+#' @param significant the features that are significant
+#' @param universe the background or universe of features measured
+#' @param annotation the annotation object
+#'
+#' @export
+#' @return hypergeometric_features-class
+hypergeometric_features = function(significant, universe, annotation) {
+  new(
+    "hypergeometric_features",
+    significant = significant,
+    universe = universe,
+    annotation = annotation
+  )
+}
+
 #' do hypergeometric enrichment
 #'
 #' @param hypergeometric_features a hypergeometric_features object