R/read-dct.R

In ayushnoori/qpcrtools: Analysis and Visualization of RT-qPCR Data

#' @include qpcr-class.R
NULL

#' Read dCT data.
#'
#' Read dCT data from qPCR experiment.
#'
#' @param file File name of dCT data in working directory, or, alternatively, path to the qPCR data file.
#' @param format Format of the data file to import. Either \code{"csv"} to specify comma-separated data,
#' or the name or index of the sheet in the Excel workbook to read the data from.
#' @param relevel Optional named list of character vectors, where names represent factors and each character vector represents the corresponding appropriate level.
#' @param ... Additional arguments to be passed to \code{data.table::fread()} or \code{openxlsx::read.xlsx()} as needed.
#' @return qPCR S4 object containing dCT data to be passed to next functions.
#' @author Ayush Noori
#' @export
read_dct = function(file, format = "csv", relevel = NULL, ...) {

  # read data
  my_dCT = if(format == "csv") fread(file, ...) else { read.xlsx(file, format, ...) %>% as.data.table() }

  # relevel as needed
  # imap(relevel, ~my_dCT[, .SD := factor(.SD, levels = .x), .SDcols = .y])

  return(my_dCT)

}