R/do_normalize.R

In nicohuttmann/pOmics: Framework for proteomics data analysis

#' Template for functions that accept either a data frame or a list
#'
#' @param data_ list or tibble
#' @param method normalisation method (see normalize())
#' @param dataset dataset
#' @param input name of input data
#' @param output name of output data
#'
#' @return
#' @export
#'
#'
do_normalize <- function(data_, method = "pqn", dataset, input, output) {

  # Handle input
  input_list <- data_input(data_ = data_, input = input)

  if (input_list[["error"]]) return(invisible(input_list[["data"]]))

  else {
    data <- input_list[["data"]]
    input <- input_list[["input"]] # Remove if not used

  }

  # Normalize data
  data <- data %>%
    tibble2matrix() %>%
    normalize(method = method) %>%
    matrix2tibble()



  # Output name
  if (!hasArg(output)) output <- input

  # Prepare return
  if (input_list[["list.input"]]) {
    data_[[output]] <- data
    attr(data_, "data") <- output
  }

  else data_ <- data

  # Return
  return(data_)

}