R/readIFC.R

In IFC: Tools for Imaging Flow Cytometry

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# This file is released under the GNU General Public License, Version 3, GPL-3 #
# Copyright (C) 2020 Yohann Demont                                             #
#                                                                              #
# It is part of IFC package, please cite:                                      #
# -IFC: An R Package for Imaging Flow Cytometry                                #
# -YEAR: 2020                                                                  #
# -COPYRIGHT HOLDERS: Yohann Demont, Gautier Stoll, Guido Kroemer,             #
#                     Jean-Pierre Marolleau, Loïc Garçon,                      #
#                     INSERM, UPD, CHU Amiens                                  #
#                                                                              #
# DISCLAIMER:                                                                  #
# -You are using this package on your own risk!                                #
# -We do not guarantee privacy nor confidentiality.                            #
# -This program is distributed in the hope that it will be useful, but WITHOUT #
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or        #
# FITNESS FOR A PARTICULAR PURPOSE. In no event shall the copyright holders or #
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# You should have received a copy of the GNU General Public License            #
# along with IFC. If not, see <http://www.gnu.org/licenses/>.                  #
################################################################################

#' @title IFC Files Generic Reader
#' @description
#' Reads IFC data from IFC files no matter if they are FCS, DAF, RIF or CIF.
#' @param fileName path to file.
#' @param ... arguments to pass to \code{\link{ExtractFromDAF}} or \code{\link{ExtractFromXIF}} or \code{\link{ExtractFromFCS}}.
#' @details If input 'fileName' is a DAF file \code{\link{ExtractFromDAF}} will be used to read the file.\cr
#' If it is a CIF or RIF file \code{\link{readIFC}} will use \code{\link{ExtractFromXIF}}.\cr
#' Finally, if 'fileName' is not a DAF, nor a CIF, nor a RIF file \code{\link{readIFC}} will use \code{\link{ExtractFromFCS}}.
#' @return an object of class `IFC_data`.
#' @examples
#' if(requireNamespace("IFCdata", quietly = TRUE)) {
#'   ## use a rif file, but you can also read daf or cif
#'   file_rif <- system.file("extdata", "example.rif", package = "IFCdata")
#'   rif <- readIFC(fileName = file_rif)
#' } else {
#'   message(sprintf('Please run `install.packages("IFCdata", repos = "%s", type = "source")` %s',
#'                   'https://gitdemont.github.io/IFCdata/',
#'                   'to install extra files required to run this example.'))
#' }
#' @export
readIFC <- function(fileName, ...) {
  file_extension = getFileExt(fileName)
  if(any(file_extension %in% c("daf", "rif", "cif"))) {
    assert(file_extension, len = 1)
    if(file_extension == "daf") return(ExtractFromDAF(fileName = fileName, ...))
    return(ExtractFromXIF(fileName = fileName, ...))
  } 
  return(ExtractFromFCS(fileName = fileName, ...))
}