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speaq (version 2.7.0)

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

Description

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) and Beirnaert et al. (2018) .

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Version

Install

install.packages('speaq')

Monthly Downloads

444

Version

2.7.0

License

Apache License 2.0

Maintainer

Charlie Beirnaert

Last Published

May 23rd, 2022

Functions in speaq (2.7.0)

HMDBsearchR

Submit 1H NMR peaks to HMDB for compound search
BWR

BW ratio calculation
AddPlottingStuff

Add plotting variables
GetWinedata.subset

Get subset of Winedata for code examples
ROIplot

Plot NMR spectra, together with raw and grouped peaks
SCANT

SCAle, Normalize and Transform a data matrix
PeakGrouper

Peak grouping with hierarchical clustering
PeakFilling

Peak filling of any missed peaks
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
Winedata

Wine dataset
SilhouetR

SilhouetR
relevant.features.p

Identify features (columns in the datamatrix) which are significantly associated with the outcome.
drawBW

BW and percentile ratios plot
returnLocalMaxima

Local maximum detection
dohClusterCustommedSegments

Use CluPA for alignment with additional information
regroupR

Regroup faulty grouped peaks
makeSimulatedData

Create a simulated NMR spectral data
doShift

Segment shift
createNullSampling

Building a null hypothesis data
dohCluster

CluPA function for multiple spectra.
hClustAlign

CluPA function for two spectra.
findRef

Reference finding
detectSpecPeaks

Peak detection for spectra
drawSpec

Spectral plot
drawSpecPPM

Plot NMR spectra from a spectra data matrix
hclust.grouping

Grouping with hierarchical clustering (used in the PeakGrouper function)
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