R/extractRownames1.R

In nicohuttmann/htmnanalysis: Analysis of Omics Data

#' Extracts row names and filters based on one column
#'
#' @param data data frame
#' @param transpose transpose data
#' @param column column to be used
#' @param lower lower or upper limit
#' @param threshold threshold for filtering
#'
#' @return
#' @export
#'
#'
extractRownames1 <- function(data, transpose = F, column, lower, threshold) {

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

  data <- transposeData(data, transpose = transpose)

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

  if(!hasArg(column)) {
    column <- whatToDo("Which column should be used for filtering?", colnames(data))
  }

  if(!hasArg(lower)) {
    lower <- ok("Is this a lower limit?")
  }


  if(!hasArg(threshold)) {
    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."))

  rownames(data)[rownames]

}