findRef: Reference finding

In speaq: Tools for Nuclear Magnetic Resonance (NMR) Spectra Alignment, Peak Based Processing, Quantitative Analysis and Visualizations

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);

speaq documentation built on May 23, 2022, 5:06 p.m.