R/normalizeSpectrum_dt.R

In pmbrophy/mzDataTable: Import and convert raw mass spectrometry data formats

#' @title Normalize a mzDt
#'
#' @description Normalize intensity of mzDt by one of the available methods.
#'   Normalization is global rather than by scan.
#'
#' @details "maxPeak": divide intensity by the max intensity. "sqrt": divide
#'   intensity using sqrt intensity transform. "sum" : divide intensity by sum
#'   intensity.
#'
#' @param mzDt the mzDt to be normalized in place
#' @param method "maxPeak", "sum", or "sqrt"
#'
#' @return returns mzDt with extra column `intensity_norm`
#'

.normalizeSpectrum_dt <- function(mzDt, method){
  intensity <- NULL
  if(method == "maxPeak"){
    #Divide each point by max intensity
    mzDt[, intensity_norm := intensity]
    
  }else if(method == "sqrt"){
    #Square root intensity transform
    mzDt[, intensity_norm := sqrt(intensity)/sqrt(sum(intensity))]
    
  }else if(method == "sum"){
    #Divide each peak by sum total intensity
    mzDt[, intensity_norm := intensity/sum(intensity)]
    
  }else if(is.null(method)){
    stop("method param is NULL")
    
  }else{
    stop("supplied method param is not supported")
    
  }
  #normalize to 1
  mzDt[, intensity_norm := intensity_norm/max(intensity_norm)]
  mzDt
}

#' @title Normalize a mzDt by seqNum
#'
#' @description Normalize intensity of each individual spectrum in the mzDt.
#'
#' @details "maxPeak": divide intensity of each spectrum by the max intensity.
#'   "sqrt": divide intensity of each spectrum using sqrt intensity transform.
#'   "sum" : divide intensity of each spectrum by sum intensity of the spectrum. 
#'
#' @param mzDt the mzDt to be normalized in place
#' @param method "maxPeak", "sum", or "sqrt"
#'
#' @return returns mzDt with extra column `intensity_norm`
#'
#'
 
.normalizeEachSpectrum_dt <- function(mzDt, method){
  intensity <- NULL
  if(method == "maxPeak"){
    #Divide each point by max intensity
    mzDt[, intensity_norm := intensity, by = seqNum]
    
  }else if(method == "sqrt"){
    #Square root intensity transform
    mzDt[, intensity_norm := sqrt(intensity)/sqrt(sum(intensity)), by = seqNum]
    
  }else if(method == "sum"){
    #Divide each peak by sum total intensity
    mzDt[, intensity_norm := intensity/sum(intensity), by = seqNum]
    
  }else if(is.null(method)){
    stop("method param is NULL")
    
  }else{
    stop("supplied method param is not supported")
    
  }
  #normalize to 1
  mzDt[, intensity_norm := intensity_norm/max(intensity_norm), by = seqNum]
  mzDt
}