# 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

## 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 |