work on find_cpts() function

R/add_snps.R

+#' Add SNPs data
+#'
+#' @param lr lr values
+#' @param path_to_snps file containing the list of SNPs (three columns needed : 'probeset_id', 'chromosome', 'position')
+#' @param rm_unknown whether or not to remove rows when 'chromosome' or 'position' is missing (defaults to TRUE)
+#'
+#' @return a [tibble()]
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' add_snps(lr, path_to_snps, rm_unknown = TRUE)
+#' }
+
+add_snps <- function(lr, path_to_snps, rm_unknown = TRUE) {
+
+  # Set NULL variables
+
+  file_name <- probeset_id <- NULL
+
+  snps <- readr::read_delim(path_to_snps) |>
+    dplyr::select(probeset_id, chromosome, position)
+
+  lr <- lr |>
+    dplyr::left_join(snps) |>
+    dplyr::select(file_name, chromosome, probeset_id, position,
+                  dplyr::everything()) |>
+    dplyr::arrange(file_name, chromosome, position)
+
+  if (rm_unknown == TRUE) {
+    lr <- lr |>
+      tidyr::drop_na(chromosome, position)
+  }
+
+  # Assign to Global Environment
+  assign(x = "lr", value = lr, pos = ".GlobalEnv")
+
+}