speaq2: Wavelet Based Tools for Feature-Wise Analysis and Quantification of Nuclear Magnetic Resonance (NMR) Spectra

Tools for feature based analysis of Nuclear Magnetic Resonance (NMR) spectra. Wavelets are used to quantify the peaks which are grouped into features with hierarchical clustering. The results can easily be incorporated in large-scale studies that include LC-MS analysis (as this is also peak/feature based).

Author
Charlie Beirnaert, Kris Laukens
Date of publication
2016-11-15 08:45:34
Maintainer
Charlie Beirnaert <charlie.beirnaert@uantwerpen.be>
License
GPL-3
Version
0.1.0

View on CRAN

Man pages

AddPlottingStuff
Add plotting variables
BuildFeatureMatrix
Build a Feature matrix from the with speaq 2.0 processed data
BuildRawDataMatrix
Build a raw data matrix (spectra) from spectra of unequal...
drawSpecPPM
Plot NMR spectra from a spectra data matrix
getWaveletPeaks
Convert raw NMR spectra to peak data by using wavelets
hclust.grouping
Realignment with hierarchical clustering (used in the...
PeakAligner
Realignment with hierarchical clustering
PeakFilling
Peak filling of any missed peaks
regroupR
Regroup faulty aligned peaks
relevant.features.p
identify features (columns in the datamatrix) which are...
SCANT
SCAle, Normalize and Transform a data matrix
SilhouetR
SilhouetR
Winedata
Wine dataset

Files in this package

speaq2
speaq2/inst
speaq2/inst/doc
speaq2/inst/doc/speaq2_illustrations.Rmd
speaq2/inst/doc/speaq2_illustrations.html
speaq2/inst/doc/speaq2_illustrations.R
speaq2/NAMESPACE
speaq2/data
speaq2/data/datalist
speaq2/data/Winedata.rda
speaq2/R
speaq2/R/SCANT.R
speaq2/R/PeakFilling.R
speaq2/R/AddPlottingStuff.R
speaq2/R/SilhouetR.R
speaq2/R/relevant.features.p.R
speaq2/R/regroupR.R
speaq2/R/BuildRawDataMatrix.R
speaq2/R/hclust.grouping.R
speaq2/R/Winedata.R
speaq2/R/drawSpecPPM.R
speaq2/R/PeakAligner.R
speaq2/R/BuildFeatureMatrix.R
speaq2/R/getWaveletPeaks.R
speaq2/vignettes
speaq2/vignettes/speaq2_illustrations.Rmd
speaq2/MD5
speaq2/build
speaq2/build/vignette.rds
speaq2/DESCRIPTION
speaq2/man
speaq2/man/relevant.features.p.Rd
speaq2/man/Winedata.Rd
speaq2/man/BuildRawDataMatrix.Rd
speaq2/man/drawSpecPPM.Rd
speaq2/man/BuildFeatureMatrix.Rd
speaq2/man/SCANT.Rd
speaq2/man/PeakFilling.Rd
speaq2/man/hclust.grouping.Rd
speaq2/man/getWaveletPeaks.Rd
speaq2/man/regroupR.Rd
speaq2/man/AddPlottingStuff.Rd
speaq2/man/SilhouetR.Rd
speaq2/man/PeakAligner.Rd