dohCluster {speaq}

CluPA function for multiple spectra.

Description

Use CluPA for alignment for multiple spectra.

Usage

dohCluster(
  X,
  peakList,
  refInd = 0,
  maxShift = 100,
  acceptLostPeak = TRUE,
  verbose = TRUE
)

Arguments

X

The spectral dataset in the matrix format in which each row contains a single sample

peakList

The peak lists of the spectra

refInd

The index of the reference spectrum.

maxShift

The maximum number of the 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.

verbose

A boolean value to allow print out process information.

Value

The aligned spectra.

Author(s)

Trung Nghia Vu

See Also

dohClusterCustommedSegments

Examples

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;
maxShift = 50;
Y <- dohCluster(X,
                peakList = peakList,
                refInd = refInd,
                maxShift  = maxShift,
                acceptLostPeak = TRUE, verbose=FALSE);