related to #24 #25 remove data documents

ytakemon · Mar 3, 2022 · b45ce51 · b45ce51
1 parent 91cd16c
commit b45ce51
Show file tree

Hide file tree

Showing 17 changed files with 10 additions and 232 deletions.
diff --git a/GINIR_data_document.tar.gz b/GINIR_data_document.tar.gz
diff --git a/R/CCLE_exp.R b/R/CCLE_exp.R
diff --git a/R/CCLE_exp_annot.R b/R/CCLE_exp_annot.R
diff --git a/R/copy_num.R b/R/copy_num.R
diff --git a/R/copy_num_annot.R b/R/copy_num_annot.R
diff --git a/R/dep.R b/R/dep.R
diff --git a/R/dep_annot.R b/R/dep_annot.R
diff --git a/R/essential_genes.R b/R/essential_genes.R
diff --git a/R/gene_effect.R b/R/gene_effect.R
diff --git a/R/list_available_cancer_type.R b/R/list_available_cancer_type.R
@@ -4,18 +4,19 @@
 #' `list_available_cancer_types()` and `list_available_cancer_subtypes()` provide tools for identifying cancer (sub)types that are available in DepMap.
 #' 
 #' @return string A vector containing unique cancer types available
-#' 
+
+#' @param data_dir string Path to GINIR_data
 #' @import rlang
 #' @import dplyr
 #' @import utils
 #' 
 #' @export
 #' @examples
 #' list_available_cancer_types()
-list_available_cancer_types <- function(){
+list_available_cancer_types <- function(data_dir){
   # Load necessary data
   sample_annot <- NULL # see: https://support.bioconductor.org/p/24756/
-  load(paste0(system.file(package = "GINIR"), "/data/sample_annot.rda"), envir = environment())
+  load(paste0(data_dir, "/sample_annot.rda"), envir = environment())
 
   # Main
   sample_annot %>% 
@@ -25,14 +26,15 @@ list_available_cancer_types <- function(){
 #' @describeIn list_available_cancer_types List cancer subtypes that are available
 #' 
 #' @param input_disease string A vector of unique with one or more cancer types listed in `list_available_cancer_types()`
+#' @param data_dir string Path to GINIR_data
 #' @importFrom rlang .data
 #' @export
 #' @examples
 #' list_available_cancer_subtypes("Lung Cancer")
-list_available_cancer_subtypes <- function(input_disease){
+list_available_cancer_subtypes <- function(input_disease, data_dir){
   # Load necessary data
   sample_annot <- NULL # see: https://support.bioconductor.org/p/24756/
-  load(paste0(system.file(package = "GINIR"), "/data/sample_annot.rda"), envir = environment())
+  load(paste0(data_dir, "/sample_annot.rda"), envir = environment())
 
   # Main
   sample_annot %>% 

diff --git a/R/mut_calls.R b/R/mut_calls.R
diff --git a/R/nonessential_genes.R b/R/nonessential_genes.R
diff --git a/R/protein.R b/R/protein.R
diff --git a/R/protein_annot.R b/R/protein_annot.R
diff --git a/R/protein_nodup.R b/R/protein_nodup.R
diff --git a/R/sample_ARID1A_KO_screen.R b/R/sample_ARID1A_KO_screen.R
diff --git a/R/sample_annot.R b/R/sample_annot.R