R/h5_read_mat.R

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

#' read a simple matrix from hdf5 file
#'
#' @param filename character specifying the file to read from
#' @return matrix read from file

h5_read_mat <- function(filename) {
    # check input parameter
  if (!is.character(filename) || !file.exists(filename)) {
      warning("Invalid filename, returning NULL")
      return(NULL)
  }
  if (exists("rnames")) {
    rm("rnames")
  }
  # list the content and load the data
  content <- rhdf5::h5ls(filename)
  if ("rownames" %in%  content$name) {
      rnames <- rhdf5::h5read(filename, "rownames")
  }
  cnames <- rhdf5::h5read(filename, "colnames")
  m <- rhdf5::h5read(filename, "data")
  if (length(cnames) == ncol(m)) {
    colnames(m) <- cnames
  }else{
    warning("Number of columns does not match colnames")
  }
  if (exists("rnames")) {
    if (length(rnames) == nrow(m)) {
      rownames(m) <- rnames
    }else{
      warning("Number of rows does not match rownames")
    }
  }

  return(m)
}