diff --git a/R/GINI_screen.R b/R/GINI_screen.R index 19db6b6..132965f 100644 --- 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$DepMap_ID] diff --git a/R/extract_protein_expr.R b/R/extract_protein_expr.R index ae731aa..9e84de6 100644 --- a/R/extract_protein_expr.R +++ b/R/extract_protein_expr.R @@ -27,7 +27,9 @@ extract_protein_expr <- function(Input_samples = NULL, Input_genes = NULL){ # Load necessary data protein_annot <- protein_nodup <- sample_annot <- NULL # see: https://support.bioconductor.org/p/24756/ - data(list = list("protein_nodup", "protein_annot", "sample_annot"), envir = environment()) + load("data/protein_nodup.rda", envir = environment()) + load("data/protein_annot.rda", envir = environment()) + load("data/sample_annot.rda", envir = environment()) # Check if inputs are recognized if(!all(Input_samples %in% sample_annot$DepMap_ID)){ diff --git a/R/extract_rna_expr.R b/R/extract_rna_expr.R index 9dd5732..24e5ffb 100644 --- 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$DepMap_ID)){ diff --git a/R/get_names.R b/R/get_names.R index 9d16fc0..6c5f595 100644 --- a/R/get_names.R +++ b/R/get_names.R @@ -17,7 +17,8 @@ get_GeneNameID <- function(GeneName){ # Load necessary data dep_annot <- CCLE_exp_annot <- NULL # see: https://support.bioconductor.org/p/24756/ - utils::data(list = list("dep_annot", "CCLE_exp_annot"), envir = environment()) + load("data/dep_annot.rda", envir = environment()) + load("data/CCLE_exp_annot.rda", envir = environment()) # For Hugo symbols/NCBI IDs - from dependency prob. if(any(dep_annot$GeneNames %in% GeneName | dep_annot$GeneID %in% GeneName)){ diff --git a/R/list_available_mutations.R b/R/list_available_mutations.R index 9004a71..b2eaa5e 100644 --- a/R/list_available_mutations.R +++ b/R/list_available_mutations.R @@ -38,7 +38,7 @@ list_available_mutations <- function(Gene = NULL, # Load necessary data mut_calls <- NULL # see: https://support.bioconductor.org/p/24756/ - data(list = list("mut_calls"), envir = environment()) + load("data/mut_calls.rda", envir = environment()) # If Gene is provided look for mutations: if(!is.null(Gene)){ diff --git a/R/select_cell_lines.R b/R/select_cell_lines.R index 7367f89..e9fddad 100644 --- a/R/select_cell_lines.R +++ b/R/select_cell_lines.R @@ -89,7 +89,11 @@ select_cell_lines <- function(Input_gene = NULL, Input_AA_change = NULL, Input_d # Load necessary data mut_calls <- copy_num_annot <- copy_num <- dep <- sample_annot <- NULL # see: https://support.bioconductor.org/p/24756/ - data(list = list("mut_calls", "copy_num_annot", "copy_num", "dep", "sample_annot"), envir = environment()) + load("data/mut_calls.rda", envir = environment()) + load("data/copy_num_annot.rda", envir = environment()) + load("data/copy_num.rda", envir = environment()) + load("data/dep.rda", envir = environment()) + load("data/sample_annot.rda", envir = environment()) # Check if input gene mutations exist if(!any(mut_calls$Hugo_Symbol %in% Input_gene)|!any(copy_num_annot$GeneNames %in% Input_gene)){