Tools for Nuclear Magnetic Resonance (NMR) Spectra Alignment, Peak Based Processing, Quantitative Analysis and Visualizations
Add plotting variables
Build a Feature matrix from the with speaq 2.0 processed data
Build a raw data matrix (spectra) from spectra of unequal length
BW ratio calculation
Building a null hypothesis data
Peak detection for spectra
CluPA function for multiple spectra.
Use CluPA for alignment with additional information
Segment shift
BW and percentile ratios plot
Spectral plot
Plot NMR spectra from a spectra data matrix
Reference finding
Selecting the peaks in a segment
Finding the shift-step by using Fast Fourier Transform cross- correlat...
Convert raw NMR spectra to peak data by using wavelets
Get subset of Winedata for code examples
Grouping with hierarchical clustering (used in the PeakGrouper functio...
CluPA function for two spectra.
Submit 1H NMR peaks to HMDB for compound search
Create a simulated NMR spectral data
Peak filling of any missed peaks
Peak grouping with hierarchical clustering
Regroup faulty grouped peaks
Identify features (columns in the datamatrix) which are significantly ...
Local maximum detection
Plot NMR spectra, together with raw and grouped peaks
SCAle, Normalize and Transform a data matrix
SilhouetR
Makes Nuclear Magnetic Resonance spectroscopy (NMR spectroscopy) data analysis as easy as possible by only requiring a small set of functions to perform an entire analysis. 'speaq' offers the possibility of raw spectra alignment and quantitation but also an analysis based on features whereby the spectra are converted to peaks which are then grouped and turned into features. These features can be processed with any number of statistical tools either included in 'speaq' or available elsewhere on CRAN. More details can be found in Vu et al. (2011) <doi:10.1186/1471-2105-12-405> and Beirnaert et al. (2018) <doi:10.1371/journal.pcbi.1006018>.