R/IMS_parallel.R

In InterpretMSSpectrum: Interpreting High Resolution Mass Spectra

#' @title IMS_parallel.
#'
#' @description \code{IMS_parallel} is a parallel implementation of \code{\link{InterpretMSSpectrum}}.
#'
#' @details For mass processing and testing it may be sufficient to use \code{InterpretMSSpectrum} 
#'     without plotting functionality. However, function is likely to be deprecated or integrated 
#'     as an option into the main function in the future.
#'
#' @param spectra List of spectra.
#' @param precursor vector of precursor masses of length(spectra).
#' @param ncores Number of cores available.
#' @param correct_peak Potentially a vector of correct Peaks, see \code{InterpretMSSpectrum} for details.
#' @param ... Further parameters passed directly to \code{InterpretMSSpectrum}.
#'
#' @return A list of \code{InterpretMSSpectrum} result objects which can be systematically evaluated. 
#'     However, note that plotting is unfortunately not enabled for parallel processing.
#'
#' @seealso \code{\link{InterpretMSSpectrum}}
#'
#' @export
#'
IMS_parallel <- function(spectra=NULL, ncores=8, precursor=NULL, correct_peak=NULL, ...) {
  
  # check for foreach and doParallel to be able to keep it in suggested packages
  check_pkg <- sapply(c("foreach", "doParallel"), requireNamespace, quietly = TRUE)
  if (!all(check_pkg)) {
    msg <- paste0(
      "The use of this function requires package", ifelse(sum(!check_pkg)>1, "s", ""),
      paste(names(check_pkg)[!check_pkg], collapse=", "),
      ". Please install."
    )
    stop(msg)
  }
  `%dopar%` <- foreach::"%dopar%"
  # dummy line to initialize idx
  idx <- NULL
  cat(paste0("\n\nStart processing of ", length(spectra), " spectra, which may take a while.\n..."))
  subset <- split(1:length(spectra), gl(ncores,ceiling(length(spectra)/ncores)))
  cl <- parallel::makeCluster(ncores)
  doParallel::registerDoParallel(cl)
  res <- foreach::foreach(idx = subset) %dopar% {
    lapply(idx, function(i) {
      cat(correct_peak[i])
      InterpretMSSpectrum::InterpretMSSpectrum(
        spec=spectra[[i]], 
        silent=TRUE, 
        precursor=precursor[i], 
        correct_peak=correct_peak[i], 
        ...
      )
    })
  }
  doParallel::stopImplicitCluster()
  invisible(unlist(res, recursive = FALSE, use.names=FALSE))
}