R/sendToMSF.r

In InterpretMSSpectrum: Interpreting High Resolution Mass Spectra

#' @name sendToMSF
#' @aliases sendToMSF
#' @aliases sendToMSF.default
#' @aliases sendToMSF.findMAIN
#' 
#' @title Exporting spectra to MSFinder.
#' 
#' @description Send spectrum to MSFinder.
#' 
#' @details In the default case 'x' can be a matrix or data frame, where the first two columns 
#'     are assumed to contain the 'mz' and 'intensity' values, respectively. Further arguments 
#'     'precursormz' and 'precursortype' are required in this case. Otherwise 'x' can be of 
#'     class \code{findMAIN}.
#' 
#' @param x A matrix or 'findMAIN' object
#' @param ... Arguments passed to methods of \code{\link{writeMSF}}.
#'
#' @return
#' Full path of generated MAT file (invisibly).

#' @examples
#' \dontrun{
#' utils::data(esi_spectrum, package = "InterpretMSSpectrum")
#' fmr <- findMAIN(esi_spectrum)
#' sendToMSF(fmr, outfile="tmp.mat")
#' sendToMSF(fmr, outfile="tmp.mat", rank=1:3)
#' }
#'
#' @rdname sendToMSF
#' @export
#' 
#' @references H.Tsugawa et al (2016) Hydrogen rearrangement rules: computational MS/MS fragmentation and structure elucidation using MS-FINDER software. Analytical Chemistry, 88, 7946-7958
#' 
sendToMSF <- function(x, ...) {
  UseMethod("sendToMSF")
}

#' @param precursormz m/z of (de)protonated molecule or adduct ion 
#' @param precursortype adduct type, e.g. \code{[M+H]+} or \code{[M+Na]+}. Accepted values are all adduct ions supported by MSFINDER.
#' @param outfile Name of MAT file. If NULL, a temporary file is created in the  per-session temporary directory (see \code{\link{tempdir}}).
#' @param MSFexe Full path of MS-FINDER executable. This needs to be set  according to your system. If \code{NULL}, MAT files are written but the program is not opened.
#'   
#' @rdname sendToMSF
#' @export
#' 
sendToMSF.default <- function(
  x, 
  precursormz,
  precursortype="[M+H]+",
  outfile=NULL, 
  MSFexe=NULL, 
  ...
) {
  if(is.null(outfile)) {
    fn <- sprintf("unknown%s_%.2f.mat", 
                  format(Sys.time(), "%Y%m%d_%H%M%OS2"),
                  x[,1][which.max(x[,2])])
    outfile <- file.path(tempdir(), fn) # use the per-session temporary dir
  }
  writeMSF.default(x=x, 
                   precursormz=precursormz, 
                   precursortype=precursortype, 
                   outfile=outfile,
                   ...)
  if(!is.null(MSFexe)) {
    system2(normalizePath(MSFexe), normalizePath(dirname(outfile)), wait=FALSE)
  }
  invisible(outfile)
}

#' @param rank Which rank from 'findMAIN' should be exported.
#' @param ms2spec An (optional) MS2 spectrum to be passed to MSFINDER. If \code{NULL}, the MS1 spectrum used by 'findMAIN' is used. If dedicated MS2 spectra are available, this option should be used.
#'   
#' @rdname sendToMSF
#' @export
#' 
sendToMSF.findMAIN <- function(
  x, 
 rank=1,
 ms2spec=NULL,
 outfile=NULL, 
 MSFexe=NULL, 
 ...
) {
  if (is.null(outfile)) {
    spec <- x[[rank]][,1:2,drop=F]
    fn <- sprintf("unknown%s_%.2f.mat", 
                  format(Sys.time(), "%Y%m%d_%H%M%OS2"),
                  attr(x[[rank]], "scores")[, "adductmz"])
    outfile <- file.path(tempdir(), fn) # use the per-session temporary dir
  }
  writeMSF.findMAIN(x=x, 
                    rank=rank,
                    ms2spec=ms2spec,
                    outfile=outfile, 
                    ...)
  if (!is.null(MSFexe)) {
    system2(normalizePath(MSFexe), normalizePath(dirname(outfile)), wait=FALSE)
  }
  invisible(outfile)
}