Add new args to bootstrap_enrichment_test 2

NathanSkene · Nov 14, 2023 · 43bf2db · 43bf2db
1 parent cccf523
commit 43bf2db
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Showing 3 changed files with 20 additions and 9 deletions.
diff --git a/R/bootstrap_enrichment_test.R b/R/bootstrap_enrichment_test.R
@@ -274,6 +274,7 @@ bootstrap_enrichment_test <- function(sct_data = NULL,
         geneSizeControl = geneSizeControl,
         controlledCT = controlledCT,
         control_network = control_network,
+        store_gene_data = store_gene_data,
         verbose = verbose
     )
     hit.cells <- sumProp$hit.cells
@@ -340,9 +341,7 @@ bootstrap_enrichment_test <- function(sct_data = NULL,
     report_results(
         results = results,
         verbose = verbose
-    )
-    #### Omit gene_data to save memory ####
-    if(isFALSE(store_gene_data)) gene_data <- NULL 
+    ) 
     #### Return results list ####
     full_results <- list(
         results = results,

diff --git a/R/get_summed_proportions.r b/R/get_summed_proportions.r
@@ -34,6 +34,7 @@ get_summed_proportions <- function(hits,
                                    geneSizeControl,
                                    controlledCT = NULL,
                                    control_network = NULL,
+                                   store_gene_data = TRUE,
                                    verbose = TRUE) {
 
     controlledCT <- fix_celltype_names(celltypes = controlledCT)
@@ -83,12 +84,16 @@ get_summed_proportions <- function(hits,
         annotLevel=annotLevel,
         no_cores=no_cores)
     #### Get gene scores #####
-    gene_data <- compute_gene_scores(sct_data = sct_data, 
-                                     annotLevel = annotLevel, 
-                                     bootstrap_list = bootstrap_list, 
-                                     hits = hits, 
-                                     combinedGenes = combinedGenes,
-                                     verbose = verbose)
+    if(isTRUE(store_gene_data)){
+      gene_data <- compute_gene_scores(sct_data = sct_data, 
+                                       annotLevel = annotLevel, 
+                                       bootstrap_list = bootstrap_list, 
+                                       hits = hits, 
+                                       combinedGenes = combinedGenes,
+                                       verbose = verbose)
+    } else {
+      gene_data <- NULL
+    } 
     #### Get celltypes scores ####
     bootstrap_data <- as.matrix(
         lapply(bootstrap_list,function(x){x$celltypes}) |>

diff --git a/man/get_summed_proportions.Rd b/man/get_summed_proportions.Rd