hClustAlign: CluPA function for two spectra.
In nghiavtr/speaq: Tools for Nuclear Magnetic Resonance Spectrum Alignment and Quantitative Analysis

Description Usage Arguments Details Value Author(s) References See Also Examples

This function implements the idea of the CluPA algorithm to align the target spectrum against the reference spectrum.

hClustAlign(refSpec,
        tarSpec,
        peakList,
        peakLabel,
        startP,
        endP,
        distanceMethod = "average",
        maxShift = 0,
        acceptLostPeak = FALSE)

`refSpec`	The reference spectrum.
`tarSpec`	The target spectrum.
`peakList`	List of peaks of the both reference and target spectra
`peakLabel`	The list of the labels of the peaks
`startP`	The starting point of the segment.
`endP`	The ending point of the segment.
`distanceMethod`	The distance method for the hierarchial clustering algorithm.
`maxShift`	The maximum number of points for a shift step.
`acceptLostPeak`	This is an option for users, TRUE is the default value. If the users believe that all the peaks in the peak list are true positive, change it to FALSE.

This function implements the idea of the CluPA algorithm to align the target spectrum against the reference spectrum.

`tarSpec`	The target spectrum after alignment
`peakList`	The peak list after alignment

Trung Nghia VU

Vu TN, Valkenborg D, Smets K, Verwaest KA, Dommisse R, Lemie're F, Verschoren A, Goethals B, Laukens K. (2011) An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data. BMC Bioinformatics. 2011 Oct 20;12:405.

dohCluster

res=makeSimulatedData();
X=res$data;
groupLabel=res$label;


peakList <- detectSpecPeaks(X,
  nDivRange = c(128),                
  scales = seq(1, 16, 2),
  baselineThresh = 50000,
  SNR.Th = -1,
    verbose=FALSE
);


resFindRef<- findRef(peakList);
refInd <- resFindRef$refInd;

tarInd=1;
refSpec=X[refInd,];
tarSpec=X[tarInd,];

mergedPeakList=c(peakList[[refInd]],peakList[[tarInd]]);
mergedPeakLabel=double(length(mergedPeakList));
for (i in 1:length(peakList[[refInd]]) ) mergedPeakLabel[i]=1;
startP=1;
endP=length(tarSpec);
res=hClustAlign(refSpec,tarSpec,mergedPeakList,mergedPeakLabel,startP,endP,
        maxShift=50,acceptLostPeak=TRUE)