speaq: an R package for 1D NMR spectra data processing

The speaq package is meant to make 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 two main possibilities for NMR spectral processing:

Raw spectra alignment & processing (speaq version <= 1.2.3)
Peak based processing (new since version 2.0)

A visual representation of what each method encompasses, and how both methods can be used together can be found in the image below. More specific information on both methods can be found in their respective publications (see References).

Workflow

Installation

From CRAN using R

install.packages("speaq")   
library("speaq")

From Github using R (with devtools):

library("devtools")
install_github("speaq","beirnaert")
library("speaq")

older versions

speaq versions <= 1.2.3 are still available at https://github.com/nghiavtr/speaq

Features

Functions include

Raw spectra
- spectra alignment (CluPA)
- quantitation (BW-ratio)
- visualizations
- etc.
Peak based approach (new since v2.0)
- peak picking (wavelets)
- grouping
- peak filling
- scaling & imputations
- differential analysis (also more than 2 groups)
- visualizations
- etc.

A minimal example

library(speaq)

# get the data. (spectra in matrix format)
spectra.matrix = as.matrix(Winedata$spectra)
ppm.vector = as.numeric(Winedata$ppm)
class.factor = as.factor(Winedata$wine.color)

# plot the spectra
drawSpecPPM(Y.spec = spectra.matrix, X.ppm = ppm.vector, groupFactor = class.vector, title = 'Example spectra')

# peak detection (the default mode is parallel)
peaks <- getWaveletPeaks(Y.spec = spectra.matrix, X.ppm = ppm.vector)  

# peak grouping
groups <- PeakGrouper(Y.peaks = peaks)

# get the feature matrix
Features <- BuildFeatureMatrix(Y.data = groups)

# this featurematrix can be processed further (scaling, transformations) or 
# analysed with the statistical tools of interest like PCA.

References

Vu TN, Valkenborg D, Smets K, Verwaest KA, Dommisse R, Lemière F, Verschoren A, Goethals B, Laukens K. An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data. BMC Bioinformatics, 2011, 12:405, doi: https://doi.org/10.1186/1471-2105-12-405

Beirnaert C, Meysman P, Vu TN, Hermans N, Apers S, Pieters L, Covaci A, Laukens K (2017) speaq 2.0: a complete workflow for high-throughput 1D NMR spectra processing and quantification. PLoS Computational Biology, 2018, doi: https://doi.org/10.1371/journal.pcbi.1006018

License

The speaq package is licensed under the Apache License v2.0

Beirnaert / speaq

readme