Release/v.0.4.1

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: icWGCNA
 Title: Iterative Correcting Weighted Gene Co-expression Network Analysis
-Version: 0.4.0
+Version: 0.4.1
 Authors@R: c(
     person("Mike", "Mason", , "mike.mason@bms.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-5652-7739")),
@@ -35,7 +35,7 @@ Suggests:
     foreach,
     ggplot2,
     mockery,
-    msigdbr,
+    msigdbdf (>= 24.1.0),
     parallel,
     purrr,
     R.utils,
@@ -52,9 +52,11 @@ Suggests:
 LinkingTo: 
     Rcpp,
     RcppEigen
-Remotes: dviraran/xCell
+Remotes: 
+    dviraran/xCell,
+    igordot/msigdbdf
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Config/testthat/parallel: true

NEWS.md

@@ -1,3 +1,8 @@
+# icWGCNA 0.4.1
+
+- Fixed bug in `map_eigengenes_on_seurat()` when cutoff method is "value"
+- Updated MSigDB data for `compute_MSigDB_enrichment()` 
+
 # icWGCNA 0.4.0
 
 ### New Features

R/downstream.R

@@ -292,7 +292,7 @@ compute_MSigDB_enrichment <- function(membership_matrix,
                                       memb_cut = .65,
                                       cats = c("H", "C3", "C6", "C7", "C8"),
                                       p_cut = 0.001) {
-  needed_packages <- c('msigdbr', 'foreach', 'tidyr')
+  needed_packages <- c('msigdbdf', 'foreach', 'tidyr')
   missing_packages <- !vapply(needed_packages,
                           FUN = requireNamespace, quietly = TRUE,
                           FUN.VALUE = logical(1))
@@ -308,8 +308,8 @@ compute_MSigDB_enrichment <- function(membership_matrix,
     stop("membership_matrix values can't be <-1 or >1")
   }
 
-  m_df_simp <- msigdbr::msigdbr(species = "Homo sapiens")
-  gs_cat_levels <- sort(unique(m_df_simp$gs_cat))
+  m_df_simp <- msigdbdf::msigdbdf(target_species = "HS")
+  gs_cat_levels <- sort(unique(m_df_simp$gs_collection))
 
   if (all(!cats %in% gs_cat_levels)) {
     stop('No "cats" found in MSigDB. Must use at least one of: ',
@@ -322,8 +322,8 @@ compute_MSigDB_enrichment <- function(membership_matrix,
   }
 
   sig_list <- lapply(cats, function(xx) {
-    tmp_data <- m_df_simp[m_df_simp$gs_cat == xx, ]
-    split(x = tmp_data$gene_symbol, f = tmp_data$gs_name)
+    tmp_data <- m_df_simp[m_df_simp$gs_collection == xx, ]
+    split(x = tmp_data$db_gene_symbol, f = tmp_data$gs_name)
   })
   names(sig_list) <- cats
 
@@ -924,7 +924,7 @@ display_top_genes <- function(
 #' results <- icwgcna(ex)
 #'
 #' unique_top_genes <- map_eigengenes_on_seurat(
-#'     SeuratObject::pbmc_small
+#'     SeuratObject::pbmc_small,
 #'     results$community_membership
 #'     )
 #' }
@@ -957,7 +957,7 @@ map_eigengenes_on_seurat <- function(
 
   message('Collecting signatures...')
 
-  if (cutoff_method %in% c('kme', 'both')) {
+  if (cutoff_method %in% c('value', 'both')) {
 
     genelist <- lapply(
       membership,

tests/testthat/test-downstream.R

@@ -136,7 +136,7 @@ test_that('requireNamespace stubbing (MSigDB)', {
 
   expect_error(
     compute_MSigDB_enrichment(testing_results$community_membership),
-    "Must have the following R packages installed for this function: msigdbr, foreach, tidyr")
+    "Must have the following R packages installed for this function: msigdbdf, foreach, tidyr")
 
 })