R/combineMS2.R

In WMBEdmands/CompMS2miner: an automatable metabolite identification, visualization and data-sharing R package for high-resolution LC-MS datasets

#' combineMS2 ions either within and/ or between composite spectra 
#' 
#' @param object. a compMS2 class object obtained from the function CompMSset
#' @param method. "Ions" intra-spectrum ions grouping or "Spectra" inter-spectra
#' ion grouping, composite spectra from multiple MS2 files matched to the same
#' MS1 feature are matched. The method "removeContam" will remove possible 
#' contaminants defined as sequences of isobars with sufficient spectral similarity
#' and seperated by a maximum retention time gap. This function can be used
#' to identify and remove before or after metabolite identification methods.#' 
#' @param ... option arguments to be passed along.
#' 
#' @return A compMS2 object with intra-composite spectrum or inter-composite 
#' spectra, grouped, signal summed and group mass-to-charge averaged spectra. 
#' @seealso \code{\link{combineMS2.Ions}}, \code{\link{combineMS2.Spectra}},
#' \code{\link{combineMS2.removeContam}}.
#' @export
setGeneric("combineMS2", function(object, ...) standardGeneric("combineMS2"))

setMethod("combineMS2", signature = "compMS2", function(object, method="Ions", ...) {
  
  method <- match.arg(method, c("Ions","Spectra", 'removeContam'))
  method <- paste("combineMS2", method, sep=".")
  invisible(do.call(method, alist(object, ...)))
})