R/h5_write_misc.R

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

#' write some input data of the benchmark to hdf5
#'
#' @param genesets list of string vectors
#' @param algorithm.names character vector;
#'  names of the deconvolution algorithms used
#' @param function.call call object
#' @param grouping numeric vector grouping samples in test and training set
#' @param filename string, where should the data be stored?
#'
#' @return NULL, function saves into ‘filename‘

write_misc_input <- function(
  genesets,
  algorithm.names,
  function.call,
  grouping,
  filename
) {
  # parameter checks
  if (!is.character(algorithm.names)) {
    stop("Invalid algorithm.names. Must be character vector.")
  }
  if (!is.call(function.call)) {
    stop("function.call must be of class call")
  }
  if ((!is.factor(grouping) || length(levels(grouping)) != 2) &&
       !is.null(grouping)) {
    stop("grouping is not valid. Must be factor with two levels")
  }
  if (!is.null(genesets)) {
    if (!is.list(genesets) ||
        !all(sapply(genesets, function(x) is.character(x)))) {
      stop("genesets must be a list of character vectors")
    }
  }

  rhdf5::h5createFile(filename)
  if (!is.null(genesets)) {
    rhdf5::h5createGroup(filename, "genesets")
    for (g in names(genesets)) {
      rhdf5::h5write(
        as.vector(genesets[[g]]),
        filename,
        paste("genesets", g, sep = "/")
      )
    }
  }
  rhdf5::h5write(as.vector(algorithm.names), filename, "algorithms")
  if (!is.null(grouping)) {
    rhdf5::h5write(as.vector(grouping), filename, "grouping")
  }
  rhdf5::h5createGroup(filename, "function_call")
  function.args <- as.character(function.call)
  function.argnames <- names(as.list(function.call))
  rhdf5::h5write(as.vector(function.args), filename, "function_call/args")
  rhdf5::h5write(
    as.vector(function.argnames), filename, "function_call/argnames"
  )
  return(NULL)
}