speaq: Tools for Nuclear Magnetic Resonance Spectrum Alignment and Quantitative Analysis

We introduce a novel suite of informatics tools for the quantitative analysis of NMR metabolomic profile data. The core of the processing cascade is a novel peak alignment algorithm, called hierarchical Cluster-based Peak Alignment (CluPA). The algorithm aligns a target spectrum to the reference spectrum in a top-down fashion by building a hierarchical cluster tree from peak lists of reference and target spectra and then dividing the spectra into smaller segments based on the most distant clusters of the tree. To reduce the computational time to estimate the spectral misalignment, the method makes use of Fast Fourier Transformation (FFT) cross-correlation. Since the method returns a high-quality alignment, we can propose a simple methodology to study the variability of the NMR spectra. For each aligned NMR data point the ratio of the between-group and within-group sum of squares (BW-ratio) is calculated to quantify the difference in variability between and within predefined groups of NMR spectra. This differential analysis is related to the calculation of the F-statistic or a one-way ANOVA, but without distributional assumptions. Statistical inference based on the BW-ratio is achieved by bootstrapping the null distribution from the experimental data. See Vu et al. (2011)<DOI:10.1186/1471-2105-12-405> for further information.

Author
Trung Nghia Vu, Kris Laukens and Dirk Valkenborg
Date of publication
2016-11-16 02:06:10
Maintainer
Trung Nghia Vu <nghiavtr@gmail.com>
License
Apache License 2.0
Version
1.2.2
URLs

View on CRAN

Man pages

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
findRef
Reference finding
findSegPeakList
Selecting the peaks in a segment
findShiftStepFFT
Finding the shift-step by using Fast Fourier Transform...
hClustAlign
CluPA function for two spectra.
makeSimulatedData
Create a simulated NMR spectral data
returnLocalMaxima
Local maximum detection
speaq-package
Tools for Nuclear Magnetic Resonance Spectrum Alignment and...

Files in this package

speaq
speaq/inst
speaq/inst/doc
speaq/inst/doc/speaq.Rnw
speaq/inst/doc/speaq.pdf
speaq/inst/doc/speaq.R
speaq/NAMESPACE
speaq/NEWS
speaq/R
speaq/R/detectSpecPeaks.R
speaq/R/dohCluster.R
speaq/R/dohClusterCustommedSegments.R
speaq/R/doShift.R
speaq/R/drawBW.R
speaq/R/BWR.R
speaq/R/drawSpec.R
speaq/R/findShiftStepFFT.R
speaq/R/makeSimulatedData.R
speaq/R/findSegPeakList.R
speaq/R/hClustAlign.R
speaq/R/findRef.R
speaq/R/createNullSampling.R
speaq/R/returnLocalMaxima.R
speaq/vignettes
speaq/vignettes/speaq.Rnw
speaq/MD5
speaq/build
speaq/build/vignette.rds
speaq/DESCRIPTION
speaq/man
speaq/man/detectSpecPeaks.Rd
speaq/man/drawBW.Rd
speaq/man/createNullSampling.Rd
speaq/man/hClustAlign.Rd
speaq/man/findSegPeakList.Rd
speaq/man/BWR.Rd
speaq/man/doShift.Rd
speaq/man/makeSimulatedData.Rd
speaq/man/findRef.Rd
speaq/man/speaq-package.Rd
speaq/man/dohCluster.Rd
speaq/man/findShiftStepFFT.Rd
speaq/man/dohClusterCustommedSegments.Rd
speaq/man/drawSpec.Rd
speaq/man/returnLocalMaxima.Rd