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

## 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