findRef: Reference finding

In nghiavtr/speaq: Tools for Nuclear Magnetic Resonance Spectrum Alignment and Quantitative Analysis

Description

This function is to heuristically detect a reference spectrum.

Usage

findRef(peakList)

Arguments

peakList

The peak lists of the spectra.

Details

This function is to heuristically detect a reference spectrum, see the reference for more details.

Value

refInd	The index of the reference spectrum found by the algorithm
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, 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.

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 1:length(resFindRef$orderSpec))
    cat(paste(i, ":",resFindRef$orderSpec[i],sep=""), " ");
    
cat("\n The reference is: ", refInd);

nghiavtr/speaq documentation built on May 20, 2019, 5:27 p.m.