replaced extract_a(), extract_b() and calculate_lr() with one function calculate_lr()

R/calculate_lr.R

-#' Calculate lr values from signal A and signal B
+#' Calculate lr values from summary file
 #'
-#' @param signal_a signal_a values
-#' @param signal_b signal_b values
+#' @param summary_file imported summary file (usually named 'summary')
+#' @param format "wide" or "long" table (defaults to "long")
 #'
 #' @import dplyr
 #' @import tidyr
@@ -11,25 +11,52 @@
 #'
 #' @examples
 #' \dontrun{
-#' calculate_lr(signal_a, signal_b)
+#' calculate_lr(summary_file, format = "long")
 #' }
 
-calculate_lr <- function(signal_a, signal_b) {
+calculate_lr <- function(summary_file, format = "long") {
 
   # Set NULL variables
 
   a <- b <- pivot_longer <- probeset_id <- NULL
 
-  # Transform to long format
+  # Extract A signal from summary file
+  message("Extracting A signal from summary file")
+  signal_a <- summary_file |>
+    dplyr::filter(!grepl(pattern = "NP", x = probeset_id)) |>
+    dplyr::filter(grepl("AX-[0-9]*-A", probeset_id)) |>
+    dplyr::mutate(probeset_id = stringr::str_remove(string = probeset_id, pattern = "-A")) |>
+    tidyr::pivot_longer(cols = -probeset_id,
+                        names_to = "file_name",
+                        values_to = "signal_a")
 
-  signal_a_lg <- signal_a %>%
-    tidyr::pivot_longer(!probeset_id, names_to = "file_name", values_to = "a")
-
-  signal_b_lg <- signal_b %>%
-    tidyr::pivot_longer(!probeset_id, names_to = "file_name", values_to = "b")
+  # Extract B signal from summary file
+  message("Extracting B signal from summary file")
+  signal_b <- summary_file |>
+    dplyr::filter(!grepl(pattern = "NP", x = probeset_id)) |>
+    dplyr::filter(grepl("AX-[0-9]*-B", probeset_id)) |>
+    dplyr::mutate(probeset_id = stringr::str_remove(string = probeset_id, pattern = "-B")) |>
+    tidyr::pivot_longer(cols = -probeset_id,
+                        names_to = "file_name",
+                        values_to = "signal_b")
 
   # Calculate lr values
-  dplyr::left_join(signal_a_lg, signal_b_lg) %>%
-    dplyr::mutate(lr = log2(sqrt(a^2 + b^2))) %>%
-    dplyr::select(-c(a, b))
+  message("Calculating lr values")
+  lr <- signal_a |>
+    dplyr::left_join(signal_b) |>
+    dplyr::mutate(lr = log2(sqrt(signal_a^2 + signal_b^2)),
+                  .keep = "unused")
+
+  # If format is set to "wide", transform the table
+  if (format == "wide") {
+    message("Pivoting output table to wide format")
+    lr <- lr |>
+      tidyr::pivot_wider(id_cols = probeset_id,
+                         names_from = file_name,
+                         values_from = lr)
+  }
+
+  # Assign to Global Environment
+  assign(x = "lr", value = lr, pos = ".GlobalEnv")
+
 }