R/extractRownames.R

In nicohuttmann/htmnanalysis: Analysis of Omics Data

#' Extracts row names and filters based on columns
#'
#' @param data data
#' @param transpose should data frame be transposed
#' @param save should vector be saved
#' @param name name to be saved as
#' @param destination where to save
#' @param return should vector be returned
#'
#' @return
#' @export
#'
#'
extractRownames <- function(data, transpose, save = T, name, destination = "dat", return = F) {

  if(!hasArg(data)) {
    data <- getData()
  }

  data <- transposeData(data, transpose = transpose)

  rownames <- rep(T, nrow(data))
  message(paste(sum(rownames), "row names in total."))

  more <- T

  while(more) {

    column <- whatToDo("Which column should be used for filtering?", colnames(data))
    lower <- ok("Is this a lower limit?")
    threshold <- getNumber("Threshold: ")

    if(lower) {
      rownames <- combineAND(rownames, data[, column] > threshold)
    }

    else {
      rownames <- combineAND(rownames, data[, column] < threshold)
    }

    message(paste(sum(rownames), "row names after filtering."))

    more <- ok("Another filtering step?")

  }


  if(save) {
    saveThis(rownames(data)[rownames], name = name, destination = destination)
  }



  if(return) {
    rownames(data)[rownames]
  }


}