fix duplicate value bug

analyses/functions/descartes-functions.R

@@ -7,6 +7,9 @@ require(tidyverse)
 #' Descartes Atlas, and returns the TPM expression values for the specified genes
 #' in the given tissue as a tibble.
 #'
+#' Note: In cases where there are multiple entries for a single gene (e.g., ALG9),
+#' only the first occurrence is returned to ensure uniqueness of gene entries.
+#'
 #' @param genes A character vector representing the gene names.
 #' @param tissue A character string representing the tissue type.
 #'
@@ -22,6 +25,10 @@ require(tidyverse)
 #'   expression_data <- get_descartes_tpm_expression(c("IGF2", "MALAT1", "H19"), "muscle")
 #'   print(expression_data)
 #' }
+#' \dontrun{
+#'   expression_data <- get_descartes_tpm_expression("ALG9", "liver")
+#'   print(expression_data) # Should show only one entry for ALG9
+#' }
 #'
 #' @export
 get_descartes_tpm_expression <- function(genes, tissue) {
@@ -36,9 +43,12 @@ get_descartes_tpm_expression <- function(genes, tissue) {
   # Read the CSV file from the URL
   expression_data <- read_csv(url, col_names = c("gene", "tpm"))
 
-  # Filter the expression data to include only the input genes
+  # Filter the expression data to include only the input genes and take the first row for each gene
   filtered_expression_data <- expression_data %>% 
-    filter(gene %in% genes)
+    filter(gene %in% genes) %>%
+    group_by(gene) %>%
+    slice_head(n = 1) %>%
+    ungroup()
 
   # Create a base tibble with all input gene names
   base_tibble <- tibble(gene = genes)
@@ -86,7 +96,7 @@ get_descartes_cell_percentage_expression <- function(genes, tissue) {
   # Construct the URL based on the tissue input
   url <- paste0(
     "https://atlas.fredhutch.org/data/bbi/descartes/human_gtex/tables/tissue_percentage/", 
-    tissue, 
+    tissue,
     ".csv"
   )