R/h5_read_misc.R

In MarianSchoen/DMC: Comparison of different Deconvolution Models in several scenarios

#' read input to benchmark function from hdf5 file
#'
#' @param filename string, which file should be read in?
#' @return list with:
#'    - 'genesets': list of string vectors
#'    - 'algorithms': vector containing algorithm names
#'    - 'grouping': numeric vector grouping samples in test and training set
#'    - 'function.call': call object

read_misc_input <- function(filename) {
  # parameter check
  if (!file.exists(filename)) {
    stop(paste("Could not find file ", filename, sep = ""))
  }

  # read the content
  content <- rhdf5::h5ls(filename)
  # extract objects as writtten by h5_write_misc
  if ("/genesets" %in% content$group) {
    genesets <- list()
    for (name in content$name[which(content$group == "/genesets")]) {
      genesets[[name]] <- rhdf5::h5read(
        filename, paste("genesets/", name, sep = "/")
      )
    }
  }else{
    genesets <- NULL
  }
  algorithms <- rhdf5::h5read(filename, "algorithms")
  if ("grouping" %in% content$name) {
    grouping <- as.factor(rhdf5::h5read(filename, "grouping"))
  }else{
    grouping <- NULL
  }
  function.call <- as.list(rhdf5::h5read(filename, "function_call/args"))
  names(function.call) <- rhdf5::h5read(filename, "function_call/argnames")
  function.call <- as.call(function.call)
  return(list(
    genesets = genesets,
    algorithms = algorithms,
    grouping = grouping,
    function.call = function.call
  ))
}