R/CpdaddPreparation.R

In b2slab/mWISE: Untargeted LC-MS data annotation

#' @name CpdaddPreparation
#' @title Function to compute a compound to adduct matrix
#' @description
#' Function \code{CpdaddPreparation} computes a matrix that allows 
#' the fast matching of a peak list 
#' to KEGG database from a data frame containing adducts and 
#' fragments information.
#' @param KeggDB
#' Data frame containing a column named Compound with KEGG 
#' identifiers and a
#' column named exact_mass with the corresponding exact masses. 
#' If NULL, the
#' database available in mWISE will be used.
#' @param Info.Add
#' Data frame with adducts and in source fragments information. 
#' The columns should be:
#' \itemize{
#' \item{name} with the name of the adduct or fragment
#' \item{nmol}{ with the number of molecules (i.e., 2M+H: nmol=2 )}
#' \item{charge}{ with the charge of the adduct or fragment 
#' (i.e., M+3H: charge=3)}
#' \item{massdiff}{ with the mass difference 
#' (i.e., M+H: massdiff=1.007276)}
#' \item{quasi}{ with a 1 if the adduct should be considered 
#' as quasi-molecular and a 0, otherwise (Optional)}
#' \item{polarity}{ with a character vector indicating the 
#' polarity of the adduct or fragment. The options are "positive" 
#' or "negative"}}
#' @param do.Par
#' TRUE if parallel computing is required. Def: TRUE.
#' @param nClust
#' Number of clusters that may be used. Def: Number of clusters - 1.
#' @return
#' Function \code{CpdaddPreparation} returns a data frame with 
#' the mass-to-charge ratio of all the KEGG compounds and
#' adducts or fragments provided in Info.Add.
#' @examples 
#' data("sample.keggDB")
#' Cpd.Add <- CpdaddPreparation(KeggDB = sample.keggDB, do.Par = FALSE)
#' @export
#' @importFrom doParallel registerDoParallel
#' @importFrom plyr ldply
#' @importFrom utils data
CpdaddPreparation <- function(KeggDB = NULL, Info.Add = NULL, 
                              do.Par = TRUE, nClust = 2) {
  if (do.Par){
    doParallel::registerDoParallel(nClust)
  }
  if (is.null(KeggDB)){
    data("KeggDB", envir=environment())
  }
  if (is.null(Info.Add)){
    data("Info.Add", envir=environment())
  }
  Cpd.Add <- plyr::ldply(seq_len(nrow(KeggDB)), function(i){
    dx <- KeggDB[i,]
    adds.mz <- ((dx$exact_mass*Info.Add$nmol)+
                  Info.Add$massdiff)/abs(Info.Add$charge)
    cpd.add <- data.frame(Compound = dx$Compound, 
                          exact_mass = dx$exact_mass, 
                          Add.name = Info.Add$name, 
                          Polarity = Info.Add$polarity, 
                          mz.Add = adds.mz)
    return(cpd.add)
  },.parallel = do.Par)
  return(Cpd.Add)
}