Merge pull request #400 from Olink-Proteomics/optimization_develop_clean

Remove duplicates functions that were moved to read_npx_utils

OlinkAnalyze/R/utils.R

@@ -1,147 +1,3 @@
-#' Help function checking that the olink_platform is acceptable.
-#'
-#' @param x The name of the Olink platform. One of `Explore 3072`, `Explore HT`,
-#' `Target 96`, `Target 48`, `Flex` or `Focus`.
-#' @param broader_platform Name of the broader Olink platform. One of `qPCR` or
-#' `NGS`.
-#'
-#' @return
-#' Nothing if platform is ok, otherwise an error.
-#'
-check_olink_platform <- function(x,
-                                 broader_platform = NULL) {
-
-  # input check ----
-
-  check_is_scalar_character(string = x,
-                            error = TRUE)
-  if (!is.null(broader_platform)) {
-    check_olink_broader_platform(x = broader_platform)
-  }
-
-  # check platform ----
-
-  # filter the global variable accepted_olink_platforms to have a collection
-  # of platforms available.
-  if (is.null(broader_platform)) {
-
-    olink_platforms <- accepted_olink_platforms
-
-  } else {
-
-    olink_platforms <- accepted_olink_platforms |>
-      dplyr::filter(.data[["broader_platform"]] == .env[["broader_platform"]])
-
-  }
-
-  # Throw an error if unexpected platform
-  if (!(x %in% olink_platforms$name)) {
-
-    cli::cli_abort(
-      message = c(
-        "x" = "Unexpected Olink platform {.arg {rlang::caller_arg(x)}}!",
-        "i" = "Expected one of: {olink_platforms$name}"
-      ),
-      call = rlang::caller_env(),
-      wrap = FALSE
-    )
-
-  }
-
-}
-
-#' Help function checking that the Olink data_type is acceptable.
-#'
-#' @param x The name of the Olink data type. One of `NPX`, `Quantified` or `Ct`.
-#' @param broader_platform Name of the broader Olink platform. One of `qPCR` or
-#' `NGS`.
-#'
-#' @return
-#' Nothing if data_type is ok, otherwise an error.
-#'
-check_olink_data_type <- function(x,
-                                  broader_platform = NULL) {
-
-  # input check ----
-
-  check_is_scalar_character(string = x,
-                            error = TRUE)
-  if (!is.null(broader_platform)) {
-    check_olink_broader_platform(x = broader_platform)
-  }
-
-  # check data_type ----
-
-  # filter the global variable accepted_olink_platforms to have a collection
-  # of data types available.
-  if (is.null(broader_platform)) {
-
-    olink_quant_methods <- accepted_olink_platforms
-
-  } else {
-
-    olink_quant_methods <- accepted_olink_platforms |>
-      dplyr::filter(
-        .data[["broader_platform"]] == .env[["broader_platform"]]
-      )
-  }
-
-  olink_quant_methods <- olink_quant_methods |>
-    dplyr::pull(
-      .data[["quant_method"]]
-    ) |>
-    unlist() |>
-    unique()
-
-  # Throw an error if unexpected data_type
-  if (!(x %in% olink_quant_methods)) {
-
-    cli::cli_abort(
-      message = c(
-        "x" = "Unexpected Olink data type {.arg {rlang::caller_arg(x)}}!",
-        "i" = "Expected one of: {olink_quant_methods}"
-      ),
-      call = rlang::caller_env(),
-      wrap = FALSE
-    )
-
-  }
-
-}
-
-#' Help function checking that the broader Olink platform is acceptable.
-#'
-#' @param x Name of the broader Olink platform. One of `qPCR` or `NGS`.
-#'
-#' @return
-#' Nothing if broader Olink platform is ok, otherwise an error.
-#'
-check_olink_broader_platform <- function(x) {
-
-  # input check ----
-
-  check_is_scalar_character(string = x,
-                            error = TRUE)
-
-  # check broader platform ----
-
-  if (!(x %in% unique(accepted_olink_platforms$broader_platform))) {
-
-    cli::cli_abort(
-      message = c(
-        "x" = "Unexpected Olink broader platform
-        {.arg {rlang::caller_arg(x)}}!",
-        "i" = "Expected one of:
-        {unique(accepted_olink_platforms$broader_platform)}"
-      ),
-      call = rlang::caller_env(),
-      wrap = FALSE
-    )
-
-  }
-
-}
-
 #' Utility function removing columns with all values NA from a tibble or an
 #' arrow object.
 #'