@@ -15,7 +15,7 @@

 #' @author Federico Marini \email{marinif@@uni-mainz.de}

 #'

 #' @importFrom AnnotationDbi Definition GOID Ontology Secondary Synonym Term

-#' @importFrom backbone backbone.extract fdsm hyperg sdsm universal

+#' @importFrom backbone backbone.extract fdsm fixedrow sdsm universal

 #' @importFrom bs4Dash bs4Card bs4DashBody bs4DashControlbar

 #' bs4DashFooter bs4DashNavbar bs4DashPage bs4DashSidebar

 #' bs4InfoBox bs4InfoBoxOutput bs4SidebarMenu

@@ -329,7 +329,7 @@ ggs_backbone <- function(res_enrich,

                          n_gs = 15,

                          gs_ids = NULL,

                          bb_on = c("genesets", "features"),

-                         bb_method = c("sdsm", "fdsm", "hyperg"),

+                         bb_method = c("sdsm", "fdsm", "fixedrow"),

                          bb_extract_alpha = 0.05,

                          bb_extract_fwer = c("none", "bonferroni", "holm"),

                          bb_fullinfo = FALSE,

@@ -350,7 +350,7 @@ ggs_backbone <- function(res_enrich,

   stopifnot(is.logical(bb_remove_singletons))

   stopifnot(is.logical(color_graph))

-  bb_method <- match.arg(bb_method, c("sdsm", "fdsm", "hyperg"))

+  bb_method <- match.arg(bb_method, c("sdsm", "fdsm", "fixedrow"))

   bb_extract_fwer <- match.arg(bb_extract_fwer, c("none", "bonferroni", "holm"))

   bb_on <- match.arg(bb_on, c("genesets", "features"))

@@ -405,7 +405,7 @@ ggs_backbone <- function(res_enrich,

   } else if (bb_method == "fixedrow") {

     bbobj <- backbone::fixedrow(bpm_for_backbone, alpha = NULL)

   }

-

+  

   bbextracted <- backbone::backbone.extract(bbobj,

     alpha = bb_extract_alpha,

     mtc = bb_extract_fwer

@@ -89,7 +89,7 @@ test_that("Backbone functionality up and running", {

     annotation_obj = anno_df,

     n_gs = 20,

     bb_on = "features",

-    bb_method = "hyperg",

+    bb_method = "fixedrow",

     bb_remove_singletons = FALSE,

     bb_fullinfo = TRUE

   )