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

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Documentation for package ‘speaq’ version 2.7.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

AddPlottingStuff	Add plotting variables
BuildFeatureMatrix	Build a Feature matrix from the with speaq 2.0 processed data
BuildRawDataMatrix	Build a raw data matrix (spectra) from spectra of unequal length
BWR	BW ratio calculation
createNullSampling	Building a null hypothesis data
detectSpecPeaks	Peak detection for spectra
dohCluster	CluPA function for multiple spectra.
dohClusterCustommedSegments	Use CluPA for alignment with additional information
doShift	Segment shift
drawBW	BW and percentile ratios plot
drawSpec	Spectral plot
drawSpecPPM	Plot NMR spectra from a spectra data matrix
findRef	Reference finding
findSegPeakList	Selecting the peaks in a segment
findShiftStepFFT	Finding the shift-step by using Fast Fourier Transform cross- correlation
getWaveletPeaks	Convert raw NMR spectra to peak data by using wavelets
GetWinedata.subset	Get subset of Winedata for code examples
hclust.grouping	Grouping with hierarchical clustering (used in the PeakGrouper function)
hClustAlign	CluPA function for two spectra.
HMDBsearchR	Submit 1H NMR peaks to HMDB for compound search
makeSimulatedData	Create a simulated NMR spectral data
PeakFilling	Peak filling of any missed peaks
PeakGrouper	Peak grouping with hierarchical clustering
regroupR	Regroup faulty grouped peaks
relevant.features.p	Identify features (columns in the datamatrix) which are significantly associated with the outcome.
returnLocalMaxima	Local maximum detection
ROIplot	Plot NMR spectra, together with raw and grouped peaks
SCANT	SCAle, Normalize and Transform a data matrix
SilhouetR	SilhouetR
Winedata	Wine dataset