Corrected garbage collection.

06-Data_integration/compute_gender_specificity.R

@@ -303,11 +303,10 @@ for (i in seq_len(length(config$integrations))) {
   # We compute the delta in both cases.
   FM_enriched <- compute_genderspecificity_scores(FM)
   MF_enriched <- compute_genderspecificity_scores(MF)
+  ##FM_enriched_FDR <- compute_genderspecificity_scores_FDR(FM)
+  ##MF_enriched_FDR <- compute_genderspecificity_scores_FDR(MF)
   rm(FM, MF)
 
-  FM_enriched_FDR <- compute_genderspecificity_scores_FDR(FM)
-  MF_enriched_FDR <- compute_genderspecificity_scores_FDR(MF)
-
   # We save the full data.
   FM_ofile <- paste0(output_data_dir, integration$name, "_", limmas[[5]]$name,
                      "_max-avg_genderspecificityscore_fulldata.tsv")

06-Data_integration/merge_and_filter_rankings.R

@@ -151,7 +151,7 @@ for (i in seq_len(length(config$integrations))) {
   # B: saving the tables (for manual exploration of the results).
   #################################################################################################
 
-  # We first add the pi values to the resuts of the male and female analyses.
+  # We first add the pi values to the results of the male and female analyses.
   res_females$pi_value <- compute_pi_values(res_females$log_fold_change,
                                             res_females$P_value)
   res_males$pi_value   <- compute_pi_values(res_males$log_fold_change,

06-Data_integration/refine_GD_rankings.R

@@ -17,8 +17,6 @@ options(bitmapType = "cairo")
 config            <- read_config(config_dirs = c("../Confs/", "./"))
 output_data_dir   <- paste0(config$global_data_dir, config$local_data_dir)
 input_data_dir    <- paste0(config$global_data_dir, config$local_input_data_dir)
-input_edata_dir   <- paste0(config$global_data_dir, config$local_exp_data_dir)
-input_rsedata_dir <- paste0(config$global_data_dir, config$local_rs_exp_data_dir)
 message(paste0("[", Sys.time(), "] Configuration done."))
 
 # ================================================================================================
@@ -93,5 +91,5 @@ for (i in seq_len(length(config$integrations))) {
 
 # We clean the workspace and log the session details for reproducibility.
 rm(i)
-rm(config, output_data_dir, input_data_dir, input_edata_dir, input_rsedata_dir)
+rm(config, output_data_dir, input_data_dir)
 sessionInfo()