R/subset_observations.R

In nicohuttmann/pOmics: Framework for proteomics data analysis

#' Removes columns from data frame based on minimum values above 0
#'
#' @param data_ data
#' @param observations observarions
#' @param observations.set observations.set
#' @param dataset dataset
#' @param input if data_ is list: name of data to use
#' @param output if data_ is list: name of output data to save in list under
#'
#' @return
#' @export
#'
#'
subset_observations <- function(data_, observations, observations.set, 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

  }



  # check dataset
  if (!hasArg(dataset)) dataset <- attr(data, "dataset")
  dataset <- get_dataset(dataset)

  # Check observations set
  observations.set <- get_observations_set(observations.set = observations.set)

  # Assemble observations
  observations <- get_observations(observations = {{observations}},
                                   observations.set = observations.set,
                                   dataset = dataset)


  data <- data %>% dplyr::filter(observations %in% !!observations)


  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_)

}