R/get_data.R

In vitalinakomashko/parallelGO: Parallel Implementation for Extraction of GO Results

# --------- read_data ----------
#' Read data with genes and gene set labels to a data frame
#'
#' \code{read_file} reads a file given a path, column names and a field
#' delimiter. For the file to be processed correctly ensure that the gene
#' identifiers are in the first columns and the set labels are in the second
#' column in the file.
#'
#' @param path Character string specifying the path to file.
#'
#' @param col_names A logical value indicating whether the file contains column
#'  names in the first line.
#'
#' @param delim Character string indicating the field separator character.
#'
#' @return Data frame with two columns, where the first column is \strong{id}
#' (gene identifiers) and the second column is \strong{set_label}
#' (gene set labels).
#'
#' @export


read_file <- function(path, col_names, delim){
  if (missing(path)) {
    stop("File path must be provided")
  } else {
    if (!file.exists(path)) {
      stop(
        crayon::red("ERROR: The file doesn't exist, please provide path to",
                    "an existing file")
        )
    } else {
      message(
        crayon::yellow("ATTENTION: For the file to be processed correctly,",
                       "ensure that the gene identifiers are in the first",
                       "column and the gene set labels are in the second column.")
      )
      if (missing(col_names)) {
        stop(
          crayon::red("Please provide TRUE (present) or FALSE (absent) for",
                         "the 'col_names' parameter.")
          )
      } else {
        col_names <- col_names
      }
      if (missing(delim)) {
        stop(
          crayon::red("Please provide a value for 'delim' parameter.")
          )
      } else {
        delim <- delim
      }
      dat <- utils::read.delim(file = path, header = col_names, sep = delim,
                        stringsAsFactors = FALSE,
                        colClasses = "character",
                        row.names = NULL)
      message(
        crayon::green("SUCCESS: Read the file'", path, "' with",
                      nrow(dat), "and", ncol(dat), "columns.")
      )
      if (ncol(dat) > 2) {
        message(
          crayon::yellow("ATTENTION: Found more than two columns in the file,",
                         "retaining only the first two.")
        )
        dat <- dat[, 1:2]
      } else if (ncol(dat) < 2) {
        stop(
          crayon::red("ERROR: Need two columns for data processing, received",
                      crayon::underline(ncol(dat)), ". Please provide a file",
                      "with two columns. First column should contain contain",
                      "gene identifiers, second column should contain set",
                      "labels.")
        )
      }
      colnames(dat) <- c("id", "set_label")
      return(dat)
    }
  }
}