fix data loading method

ytakemon · Mar 2, 2022 · 6e9ddfb · 6e9ddfb
1 parent d16ae8b
commit 6e9ddfb
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Showing 6 changed files with 16 additions and 6 deletions.
diff --git a/R/GINI_screen.R b/R/GINI_screen.R
@@ -98,7 +98,8 @@ GINI_screen <- function(control_IDs = NULL, mutant_IDs = NULL, core_num = NULL,
 
   # Load necessary data
   dep <- dep_annot <- NULL # see: https://support.bioconductor.org/p/24756/
-  data(list = list("dep", "dep_annot"), envir = environment())
+  load("data/dep.rda", envir = environment())
+  load("data/dep_annot.rda", envir = environment())
 
   # Check to see if enough samples were given after filtering:
   Control_group_avail <- control_IDs[control_IDs %in% dep$DepMap_ID]

diff --git a/R/extract_protein_expr.R b/R/extract_protein_expr.R
@@ -27,7 +27,9 @@ extract_protein_expr <- function(Input_samples = NULL, Input_genes = NULL){
 
   # Load necessary data
   protein_annot <- protein_nodup <- sample_annot <- NULL # see: https://support.bioconductor.org/p/24756/
-  data(list = list("protein_nodup", "protein_annot", "sample_annot"), envir = environment())
+  load("data/protein_nodup.rda", envir = environment())
+  load("data/protein_annot.rda", envir = environment())
+  load("data/sample_annot.rda", envir = environment())
 
   # Check if inputs are recognized 
   if(!all(Input_samples %in% sample_annot$DepMap_ID)){

diff --git a/R/extract_rna_expr.R b/R/extract_rna_expr.R
@@ -26,7 +26,9 @@ extract_rna_expr <- function(Input_samples = NULL, Input_genes = NULL){
 
   # Load necessary data
   CCLE_exp <- CCLE_exp_annot <- sample_annot <- NULL # see: https://support.bioconductor.org/p/24756/
-  data(list = list("CCLE_exp", "CCLE_exp_annot", "sample_annot"), envir = environment())
+  load("data/CCLE_exp.rda", envir = environment())
+  load("data/CCLE_exp_annot.rda", envir = environment())
+  load("data/sample_annot.rda", envir = environment())
 
   # Check if inputs are recognized 
   if(!all(Input_samples %in% sample_annot$DepMap_ID)){

diff --git a/R/get_names.R b/R/get_names.R
@@ -17,7 +17,8 @@
 get_GeneNameID <- function(GeneName){
   # Load necessary data
   dep_annot <- CCLE_exp_annot <- NULL # see: https://support.bioconductor.org/p/24756/
-  utils::data(list = list("dep_annot", "CCLE_exp_annot"), envir = environment())
+  load("data/dep_annot.rda", envir = environment())
+  load("data/CCLE_exp_annot.rda", envir = environment())
 
   # For Hugo symbols/NCBI IDs - from dependency prob.
   if(any(dep_annot$GeneNames %in% GeneName | dep_annot$GeneID %in% GeneName)){

diff --git a/R/list_available_mutations.R b/R/list_available_mutations.R
@@ -38,7 +38,7 @@ list_available_mutations <- function(Gene = NULL,
 
   # Load necessary data
   mut_calls <- NULL # see: https://support.bioconductor.org/p/24756/
-  data(list = list("mut_calls"), envir = environment())
+  load("data/mut_calls.rda", envir = environment())
 
   # If Gene is provided look for mutations:
   if(!is.null(Gene)){

diff --git a/R/select_cell_lines.R b/R/select_cell_lines.R
@@ -89,7 +89,11 @@ select_cell_lines <- function(Input_gene = NULL, Input_AA_change = NULL, Input_d
 
     # Load necessary data
     mut_calls <- copy_num_annot <- copy_num <- dep <- sample_annot <- NULL # see: https://support.bioconductor.org/p/24756/
-    data(list = list("mut_calls", "copy_num_annot", "copy_num", "dep", "sample_annot"), envir = environment())
+    load("data/mut_calls.rda", envir = environment())
+    load("data/copy_num_annot.rda", envir = environment())
+    load("data/copy_num.rda", envir = environment())
+    load("data/dep.rda", envir = environment())
+    load("data/sample_annot.rda", envir = environment())
 
     # Check if input gene mutations exist
     if(!any(mut_calls$Hugo_Symbol %in% Input_gene)|!any(copy_num_annot$GeneNames %in% Input_gene)){