findRef {speaq} | R Documentation |
Reference finding
Description
This function is to heuristically detect a reference spectrum.
Usage
findRef(peakList)
Arguments
peakList |
The peak lists of the spectra. |
Value
list of 2: refInd (The index of the reference spectrum found by the algorithm) and orderSpec (A sorted array of the spectra by their goodness values)
Author(s)
Trung Nghia Vu
References
Vu TN, Valkenborg D, Smets K, Verwaest KA, Dommisse R, Lemi\'ere 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.
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
);
cat("\n Find the spectrum reference...")
resFindRef<- findRef(peakList);
refInd <- resFindRef$refInd;
cat("\n Order of spectrum for reference \n");
for (i in seq_along(resFindRef$orderSpec))
cat(paste(i, ":",resFindRef$orderSpec[i],sep=""), " ");
cat("\n The reference is: ", refInd);
[Package speaq version 2.7.0 Index]