Merge branch 'main' into handle_lm_issue

DESCRIPTION

@@ -34,8 +34,9 @@ Imports:
     janitor,
     broom,
     utils,
-    stats, 
-    stringr
+    stats,
+    stringr,
+    fastmap (>= 1.2.0)
 Suggests:
     testthat (>= 3.0.0),
     roxygen2,

R/00-setup_data.R

@@ -1,3 +1,4 @@
+
 #' Making a new gimap dataset
 #' @description This function allows people to have their data ready to be processed by gimap
 #' @param counts a matrix of data that contains the counts where rows are each paired_guide target and columns are each sample

R/03-annotate.R

@@ -62,6 +62,8 @@ gimap_annotate <- function(.data = NULL,
     dplyr::filter(stripped_cell_line_name == toupper(cell_line)) %>%
     dplyr::pull(DepMap_ID)
 
+  if (length(my_depmap_id) == 0) stop("The cell line specified, ", cell_line, "was not found in the DepMap data. Run supported_cell_lines() to see the full list")
+
   tpm_file <- file.path(system.file("extdata", package = "gimap"), "CCLE_expression.csv")
 
   if (!file.exists(tpm_file)) tpm_setup()
@@ -245,3 +247,20 @@ crtl_genes <- function() {
 
   return(crtl_genes$gene_symbol)
 }
+
+
+#' List the supported cell lines
+#' @description This function downloads the metadata for DepMap and lists which cell lines are supported.
+#' @export
+#' @examples \dontrun{
+#'
+#' cell_lines <- supported_cell_lines()
+#'
+#' }
+supported_cell_lines <- function() {
+
+ depmap_metadata <- readr::read_csv("https://figshare.com/ndownloader/files/35020903", show_col_types = FALSE)
+
+ return(sort(depmap_metadata$stripped_cell_line_name))
+
+}