comparison nmr_alignement/NmrAlignment_script.R @ 4:265ee538e120 draft default tip

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3:f3ec6799c435

    pList[[i]] = sort(unique(pList[[i]]))
    pList[[i]] = pList[[i]][which(X[i, pList[[i]]] > baselineThresh)]
    pList[[i]] = sort(pList[[i]])
    if (verbose) 
      cat("\n Spectrum ", i, " has ", length(pList[[i]]), 
          " peaks")
  }
  return(pList)
}


################################################################################################

################################################################################################
cluPA.alignment <- function(data, reference=reference, nDivRange, scales = seq(1, 16, 2), baselineThresh,  SNR.Th = -1, maxshift=maxshift, 
                            verbose)
{
  ## Peak picking
  cat("\n detect peaks....")
  startTime <- proc.time()
  peakList <- detectSpecPeaks(X=data, nDivRange=nDivRange, scales=scales, baselineThresh=baselineThresh,  
                              SNR.Th = SNR.Th, verbose=verbose)
  endTime <- proc.time()
  cat("Peak detection time:",(endTime[3]-startTime[3])/60," minutes")

  ## Reference spectrum determination
  if (reference == 0)
  {
    cat("\n Find the spectrum reference...")
    resFindRef<- findRef(peakList)
    refInd <- resFindRef$refInd
    cat("\n Order of spectrum for reference \n")
    for (i in 1:length(resFindRef$orderSpec))
    {
      cat(paste(i, ":",resFindRef$orderSpec[i],sep=""), " ")
      if (i %% 10 == 0) 
        cat("\n")
    }
    cat("\n The reference is: ", refInd)
  }
  else
  {
    refInd=reference
  }
  ## Spectra alignment to the reference
  maxshift <- 50
  Y <- dohCluster(data, peakList=peakList, refInd=refInd, maxShift=maxShift, acceptLostPeak, verbose)

  ## Output  
  return(Y)
}

4:265ee538e120

    pList[[i]] = sort(unique(pList[[i]]))
    pList[[i]] = pList[[i]][which(X[i, pList[[i]]] > baselineThresh)]
    pList[[i]] = sort(pList[[i]])
    if (verbose) 
      cat("\n Spectrum ", i, " has ", length(pList[[i]]), 
          " peaks \n")
      cat(myPeakRes)
  }
  cat("\n")
  return(pList)
}


################################################################################################

################################################################################################
cluPA.alignment <- function(data, reference=reference, nDivRange, scales = seq(1, 16, 2), baselineThresh,  SNR.Th = -1, maxshift=maxshift, 
                            verbose)
{
  ## Peak picking
  cat("\t PEAK DETECTION \n")
  startTime <- proc.time()
  peakList <- detectSpecPeaks(X=data, nDivRange=nDivRange, scales=scales, baselineThresh=baselineThresh,  
                              SNR.Th = SNR.Th, verbose=verbose)
  endTime <- proc.time()
  cat("\t Peak detection time:",(endTime[3]-startTime[3])/60," minutes \n")
  cat("\n")

  ## Reference spectrum determination
  if (reference == 0)
  {
    cat("\t DETERMINATION OF THE REFERENCE SPECTRUM \n")
    resFindRef <- findRef(peakList)
    refInd <- resFindRef$refInd
    cat("\n Order of spectrum for reference \n")
    for (i in 1:length(resFindRef$orderSpec))
    {
      cat(paste(i, ":",resFindRef$orderSpec[i],sep=""), " ")
      if (i %% 10 == 0) 
        cat("\n")
    }
	cat("\n")
	cat("\t Reference spectrum:", refInd, "\n")
    cat("\n")
  }
  else
  {
    refInd=reference
  }
  ## Spectra alignment to the reference
  cat("\t SPECTRA ALIGNMENT")
  maxshift <- 50
  Y <- dohCluster(data, peakList=peakList, refInd=refInd, maxShift=maxShift, acceptLostPeak, verbose)
  cat("\n")

  ## Output  
  return(Y)
}