R/getASSIST.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) 2021 Yohann Demont                                             #
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# It is part of IFC package, please cite:                                      #
# -IFC: An R Package for Imaging Flow Cytometry                                #
# -YEAR: 2021                                                                  #
# -COPYRIGHT HOLDERS: Yohann Demont, Jean-Pierre Marolleau, Loïc Garçon,       #
#                     CHU Amiens                                               #
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#' @title ASSIST Database Extraction
#' @description
#' Retrieves ASSIST tests values stored within .cif / .rif files.
#' @param fileName path to file..
#' @param ... other arguments to be passed.
#' @return a list of class `IFC_assist` of parsed ASSIST tests database.
#' @keywords internal
getASSIST <- function(fileName, ...) {
  dots = list(...)
  IFD = getIFD(fileName = fileName, offsets = "first", trunc_bytes = 8, force_trunc = FALSE, 
               verbose = FALSE, verbosity = 1, display_progress = FALSE, bypass = TRUE, ...)
  tmp_ass = read_xml(getFullTag(IFD = IFD, which = 1, tag = "33064", raw = TRUE), options=c("HUGE","RECOVER","NOENT","NOBLANKS","NSCLEAN"))
  return(structure(lapply(as_list(xml_find_first(tmp_ass, "//ASSISTDb")), unlist), class = c("list", "IFC_assist")))
}