R/fun_enrich_t_test.R

In nicohuttmann/pOmics: Framework for proteomics data analysis

#' Functional enrichment of t.test results
#'
#' @param data_ list or tibble
#' @param ... additional arguments to fun_enrich
#' @param view view results
#' @param dataset dataset
#' @param input name of input data
#' @param output name of output data
#'
#' @return
#' @export
#'
#'
fun_enrich_t.test <- function(data_,
                              ...,
                              view = F,
                              dataset,
                              input = "data_t.test",
                              output = "fun_enrich_t.test") {

  # 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

  }


  # Upregulated proteins

  data_fun_enrich <- list()

  data_fun_enrich[["up"]] <- fun_enrich(
    proteins = data %>%
      dplyr::filter(regulated == "up") %>%
      pull("variables"),
    background = data %>%
      pull("variables"),
    view = view,
    ...)

  data_fun_enrich[["down"]] <- fun_enrich(
    proteins = data %>%
      dplyr::filter(regulated == "down") %>%
      pull("variables"),
    background = data %>%
      pull("variables"),
    view = view,
    ...)

  #barplot(data_fun_enrich[["down"]][["KEGG"]])




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

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

  else data_ <- data

  # Return
  return(data_)

}