Package: mrbin 1.7.3

mrbin: Metabolomics Data Analysis Functions

A collection of functions for processing and analyzing metabolite data. The namesake function mrbin() converts 1D or 2D Nuclear Magnetic Resonance data into a matrix of values suitable for further data analysis and performs basic processing steps in a reproducible way. Negative values, a common issue in such data, can be replaced by positive values (<doi:10.1021/acs.jproteome.0c00684>). All used parameters are stored in a readable text file and can be restored from that file to enable exact reproduction of the data at a later time. The function fia() ranks features according to their impact on classifier models, especially artificial neural network models.

Authors:Matthias Klein [aut, cre]

mrbin_1.7.3.tar.gz
mrbin_1.7.3.zip(r-4.5)mrbin_1.7.3.zip(r-4.4)mrbin_1.7.3.zip(r-4.3)
mrbin_1.7.3.tgz(r-4.4-any)mrbin_1.7.3.tgz(r-4.3-any)
mrbin_1.7.3.tar.gz(r-4.5-noble)mrbin_1.7.3.tar.gz(r-4.4-noble)
mrbin_1.7.3.tgz(r-4.4-emscripten)mrbin_1.7.3.tgz(r-4.3-emscripten)
mrbin.pdf |mrbin.html
mrbin/json (API)
NEWS

# Install 'mrbin' in R:
install.packages('mrbin', repos = c('https://kleinomicslab.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/kleinomicslab/mrbin/issues

On CRAN:

artificial-neural-networksfeature-extractionmetabolomicsnmr

4.00 score 2 stars 2 scripts 856 downloads 49 exports 0 dependencies

Last updated 2 years agofrom:4a67ad256d. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 09 2024
R-4.5-winNOTENov 09 2024
R-4.5-linuxNOTENov 09 2024
R-4.4-winNOTENov 09 2024
R-4.4-macNOTENov 09 2024
R-4.3-winNOTENov 09 2024
R-4.3-macNOTENov 09 2024

Exports:addToPlotannotatemrbinatnvcheckmrbincontMincontPluscreatemrbincropNMRdilutionCorrectiondowneditmetabolitesmrbineditmrbinfiagetEnvintMinintPlusleftlogTrafometadatamrbinmrbinmrbinrunmrplotplotMultiNMRplotNMRplotPCAplotResultsPQNScalingpredictWrapperprintParametersputToEnvreadBrukerrecreatemrbinremoveFromPlotremoveNoiseremoveSpectrumresetEnvrightsetCurrentSpectrumsetDilutionFactorssetNoiseLevelssetOffsetsetParamtimeStampMrbintrimZerosunitVarianceScalingupzoomzoomInzoomOut

Dependencies:

mrbin

Rendered frommrbin.Rnwusingutils::Sweaveon Nov 09 2024.

Last update: 2023-03-14
Started: 2020-06-01

Readme and manuals

Help Manual

Help pageTopics
A function for adding NMR spectra to the plot list.addToPlot
A function for annotating mrbin objects.annotatemrbin
A function replacing negative values.atnv
A function for checking mrbin objects.checkmrbin
A function for changing plotNMR plots.contMin
A function for changing plotNMR plots.contPlus
A function for creating mrbin objects.createmrbin
A function for cropping HSQC spectra.cropNMR
A function for scaling to individual dilution factors.dilutionCorrection
A function for changing plotNMR plots.down
A function for editing metabolite identities.editmetabolitesmrbin
A function for editing mrbin objects.editmrbin
A function identifying features of importance.fia
A function for saving the package environment.getEnv
A function for changing plotNMR plots.intMin
A function for changing plotNMR plots.intPlus
A function for changing plotNMR plots.left
A function for log transforming data.logTrafo
A function for interactively editing metadata of mrbin objects.metadatamrbin
A function setting the parameters and performing binning and data processingmrbin
A function performing all data read and processing steps.mrbinrun
A function for plotting NMR spectra.mrplot
A function for plotting NMR spectra.plotMultiNMR
A function for plotting NMR spectra.plotNMR
A function for plotting PCA plots.plotPCA
A function for plotting quality indicators, including PCA plots.plotResults
A function for PQN scaling.PQNScaling
A function returning predicted values for use with the fia function.predictWrapper
A function for printing parameters to the screen.printParameters
A function for changing and adding variables in the package environment.putToEnv
A function for reading Bruker NMR spectra.readBruker
A function recreating parameters from previous runs.recreatemrbin
A function for removing NMR spectra from the plot list.removeFromPlot
A function for removing bins below noise level.removeNoise
A function for removing a spectrum.removeSpectrum
A parameter resetting functionresetEnv
A function for changing plotNMR plots.right
A function for interactively setting the current spectrum.setCurrentSpectrum
A function for setting dilution factors.setDilutionFactors
A function for setting and plotting noise levels.setNoiseLevels
A function for changing plotNMR plots.setOffset
A function setting parameters and checking for consistency.setParam
A function for time stamping mrbin objects.timeStampMrbin
A function for trimming zero-values bins.trimZeros
A function for scaling to unit variance.unitVarianceScaling
A function for changing plotNMR plots.up
A function for changing plotNMR plots.zoom
A function for changing plotNMR plots.zoomIn
A function for changing plotNMR plots.zoomOut