Camera_Function.R

#title: "Camera_Function"
#author: "Laura Hmelo"
#date: "December 19, 2016"

#This function processes an xcmsSet object using CAMERA to identify mass features which are related to one another as adducts or isotopomers.
#
#Input:
#1. a processed xset object from xcmsfunction.  Should be called xset3.
#
#Output:
#1. A list (CAMERAlist) containing [[1]] a processed peak list containing information about adducts, isotopes and neutral masses (xset.annot) and [[2]], a CAMERA object (xsaFA).

#Mode is "positive" or "negative". Default is positive

#setwd(outputpath)

camera <- function(xset, Polarity ="positive", PPM = 5) {
  
  library(CAMERA)
  library(snow)
  
  xsa <- xsAnnotate(xset)
  
  xsaF <- groupFWHM(xsa, perfwhm = 0.6)
  
  # peak group verification with peakshape correlation (groupCorr); slow step----
  
  xsaC <- groupCorr(xsaF)
  
  #annotation of possible isotopes (findIsotopes)----
  xsaFI <- findIsotopes(xsaC, ppm = PPM)
  
  #annotation of adducts and calculating hypothetical masses for the group; very slow step---- 
  #use xsaFA object to visualize EICs
  
  xsaFA <- findAdducts(xsaFI, ppm = PPM, polarity = Polarity)
  
  # Make a table of the annotated peaks-------
  xset.annot <- getPeaklist(xsaFA)
  
  CAMERAlist <- list(xset.annot, xsaFA)
  
  return(invisible(CAMERAlist))
  
}