fix

R/Append_perm_pval.R

@@ -1,11 +1,11 @@
 #' @title Appends permutation adjusted p-value
 #' 
-#' @description Randomly samples dependency probabilities from a given mutant and control group screened.
+#' @description Appends permutation adjusted p-values to new column.
 #' 
-#' @param p_value dataframe, Output from GI_screen(), Default: NULL
-#' @param perm_pvalues dataframe, Output from GI_screen_perms(), Default: NULL
+#' @param GI_screen_res dataframe, Output from GI_screen(), Default: NULL
+#' @param perms dataframe, Output from Pval_perm_adjust(), Default: NULL
 #' 
-#' @return A vector of adjusted p-values
+#' @return A dataframe with permutation adjusted p-values appeneded as a new column named Pval_perm_adj.
 #' 
 #' @details P-values are adjusted based on permuted random sampled background data. 
 #' @md

R/list_cancer_type.R

@@ -58,11 +58,15 @@ list_cancer_subtypes <- function(input_disease, data_dir) {
   load(paste0(data_dir, "/sample_annot.rda"), envir = environment())
 
   # Main
-  sample_annot %>%
+  res <- sample_annot %>%
     dplyr::filter(.data$disease %in% input_disease) %>%
     dplyr::pull(.data$disease_subtype) %>%
     unique
 
   # Message:
   message("See sample_annot.rda in your data directory for a complist list of cell line annotation.")
+
+  # result
+  return(res)
+
 }

R/select_cell_lines.R

@@ -194,8 +194,8 @@ select_cell_lines <- function(input_gene = NULL, input_aa_change = NULL, input_d
           .data$GT == "1|1" ~ "Hom_mut",
           TRUE ~ "Het_Mut"),
           AC_Variant = paste0(.data$VariantInfo," ", .data$AC_Variant)) %>% # are there any with 0 contribution from reference?
-        dplyr::rename(Chromosome = Chrom, Start_position = Pos) %>%
-        dplyr::select(.data$DepMap_ID, .data$Hugo_Symbol, .data$Chromosome, .data$Start_position, .data$Ref:.data$EntrezGeneID, AC_Variant) %>%
+        dplyr::rename(Chromosome = .data$Chrom, Start_position = .data$Pos) %>%
+        dplyr::select(.data$DepMap_ID, .data$Hugo_Symbol, .data$Chromosome, .data$Start_position, .data$Ref:.data$EntrezGeneID, .data$AC_Variant) %>%
         dplyr::arrange(.data$Start_position) %>% 
         dplyr::distinct()
     }
@@ -301,16 +301,16 @@ select_cell_lines <- function(input_gene = NULL, input_aa_change = NULL, input_d
         # If post23Q
         temp_dels <- target_mut %>% 
           dplyr:: filter(
-            LikelyLoF) %>% 
+            .data$LikelyLoF) %>% 
           dplyr::distinct()
 
         if(any(str_detect(temp_dels$VariantInfo, "splice"))){
           no_splice <- temp_dels %>% 
-            dplyr::filter(!str_detect(VariantInfo, "splice"))
+            dplyr::filter(!str_detect(.data$VariantInfo, "splice"))
 
           del_splice <- temp_dels %>% 
-            dplyr::filter(str_detect(VariantInfo, "splice"),
-                          VariantType != "SNV")
+            dplyr::filter(str_detect(.data$VariantInfo, "splice"),
+                          .data$VariantType != "SNV")
           mut_dels <- dplyr::bind_rows(no_splice, del_splice) %>%
             distinct()
         } else{
@@ -343,9 +343,9 @@ select_cell_lines <- function(input_gene = NULL, input_aa_change = NULL, input_d
           dplyr::filter(.data$n > 1)
       } else {
         multi_mut_dels <- mut_dels %>% 
-          dplyr::select(.data$DepMap_ID, Start_position, .data$GT) %>%
+          dplyr::select(.data$DepMap_ID, .data$Start_position, .data$GT) %>%
           dplyr::filter(.data$GT != "1|1") %>% 
-          dplyr::select(.data$DepMap_ID, Start_position) %>%
+          dplyr::select(.data$DepMap_ID, .data$Start_position) %>%
           dplyr::distinct() %>%
           dplyr::add_count(.data$DepMap_ID) %>% 
           dplyr::filter(.data$n > 1)

tests/testthat/test-list_cancer_types.R

@@ -6,6 +6,6 @@ test_that("Test that list_available_cancer_types works", {
   expect_equal(length(res1), 33)
 
   # To list all subtypes
-  res2 <- list_cancer_subtypes("Lung Cancer", data_dir = dir)
+  res2 <- list_cancer_subtypes(input_disease = "Lung Cancer", data_dir = dir)
   expect_equal(length(res2), 11)
 })