Introduction | Setup | MALDIquant objects | Workflow | Summary | Session Information
Package: MALDIquant 1.22.3
MALDIquant: Quantitative Analysis of Mass Spectrometry Data
A complete analysis pipeline for matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) and other two-dimensional mass spectrometry data. In addition to commonly used plotting and processing methods it includes distinctive features, namely baseline subtraction methods such as morphological filters (TopHat) or the statistics-sensitive non-linear iterative peak-clipping algorithm (SNIP), peak alignment using warping functions, handling of replicated measurements as well as allowing spectra with different resolutions.
Authors:
MALDIquant_1.22.3.tar.gz
MALDIquant_1.22.3.zip(r-4.7)MALDIquant_1.22.3.zip(r-4.6)MALDIquant_1.22.3.zip(r-4.5)
MALDIquant_1.22.3.tgz(r-4.6-x86_64)MALDIquant_1.22.3.tgz(r-4.6-arm64)MALDIquant_1.22.3.tgz(r-4.5-x86_64)MALDIquant_1.22.3.tgz(r-4.5-arm64)
MALDIquant_1.22.3.tar.gz(r-4.7-arm64)MALDIquant_1.22.3.tar.gz(r-4.7-x86_64)MALDIquant_1.22.3.tar.gz(r-4.6-arm64)MALDIquant_1.22.3.tar.gz(r-4.6-x86_64)
MALDIquant_1.22.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MALDIquant/json (API)
| # Install 'MALDIquant' in R: |
| install.packages('MALDIquant', repos = c('https://sgibb.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/sgibb/maldiquant/issues
Datasets:
- fiedler2009subset - Example Mass Spectra
Last updated from:3882daeba5. Checks:13 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 139 | ||
| linux-devel-x86_64 | OK | 173 | ||
| source / vignettes | OK | 206 | ||
| linux-release-arm64 | OK | 134 | ||
| linux-release-x86_64 | OK | 127 | ||
| macos-release-arm64 | OK | 116 | ||
| macos-release-x86_64 | OK | 195 | ||
| macos-oldrel-arm64 | OK | 131 | ||
| macos-oldrel-x86_64 | OK | 219 | ||
| windows-devel | OK | 112 | ||
| windows-release | OK | 105 | ||
| windows-oldrel | OK | 106 | ||
| wasm-release | OK | 95 |
Exports:alignSpectraas.matrixaverageMassSpectrabinPeakscalibrateIntensitycoordinatescoordinates<-createMassPeakscreateMassSpectrumdetectPeaksdetermineWarpingFunctionsestimateBaselineestimateNoisefilterPeaksfindEmptyMassObjectsintensityintensity<-intensityMatrixisEmptyisMassPeaksisMassPeaksListisMassSpectrumisMassSpectrumListisRegularlabelPeakslinesmassmass<-match.closestmergeMassPeaksmetaDatametaData<-monoisotopicPeaksmsiSlicesmzmz<-plotplotMsiSlicepointsreferencePeaksremoveBaselineremoveEmptyMassObjectssmoothIntensitysnrtotalIonCurrenttransformIntensitytrimwarpMassPeakswarpMassSpectra
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Quantitative Analysis of Mass Spectrometry Data | MALDIquant-package MALDIquant |
| Class "AbstractMassObject" | AbstractMassObject-class as.matrix,AbstractMassObject-method coordinates coordinates,AbstractMassObject-method coordinates,list-method coordinates<- coordinates<-,AbstractMassObject,matrix-method coordinates<-,AbstractMassObject,numeric-method coordinates<-,list,matrix-method intensity intensity,AbstractMassObject-method intensity<- intensity<-,AbstractMassObject,numeric-method isEmpty isEmpty,AbstractMassObject-method length,AbstractMassObject-method lines,AbstractMassObject-method mass mass,AbstractMassObject-method mass<- mass<-,AbstractMassObject,numeric-method metaData metaData,AbstractMassObject-method metaData<- metaData<-,AbstractMassObject-method mz mz,AbstractMassObject-method mz<- mz<-,AbstractMassObject,numeric-method points,AbstractMassObject-method [,AbstractMassObject,logical,missing-method [,AbstractMassObject,numeric,missing-method [,MassPeaks,logical,missing-method [,MassPeaks,numeric,missing-method |
| Align MassSpectrum objects. | alignSpectra |
| Averages 'MassSpectrum' objects. | averageMassSpectra |
| Align Peaks into discrete bins. | binPeaks |
| Calibrates intensities of a MassSpectrum object. | calibrateIntensity calibrateIntensity,list-method calibrateIntensity,MassSpectrum-method |
| Creates a MassPeaks object. | createMassPeaks |
| Creates a MassSpectrum object. | createMassSpectrum |
| Detects peaks in a MassSpectrum object. | detectPeaks detectPeaks,list-method detectPeaks,MassSpectrum-method |
| Determine warping functions of MassPeaks objects. | determineWarpingFunctions |
| Estimates the baseline of a MassSpectrum object. | estimateBaseline estimateBaseline,MassSpectrum-method |
| Estimates the noise of a MassSpectrum object. | estimateNoise estimateNoise,MassSpectrum-method |
| Example Mass Spectra (raw) | fiedler2009subset |
| Removes less frequent peaks. | filterPeaks |
| Finds or removes empty AbstractMassObject objects in a list. | findEmptyMassObjects removeEmptyMassObjects |
| Converts a list of MassPeaks objects into a matrix. | intensityMatrix |
| Tests for MassSpectrum or MassPeaks object. | isMassPeaks isMassSpectrum |
| Tests a list of MassSpectrum or MassPeaks objects. | isMassPeaksList isMassSpectrumList |
| Draws peak labels to plot. | labelPeaks labelPeaks,MassPeaks-method |
| Parallel Support in Package 'MALDIquant' | MALDIquant-parallel |
| Class "MassPeaks" | MassPeaks MassPeaks-class snr snr,MassPeaks-method |
| Class "MassSpectrum" | isRegular isRegular,MassSpectrum-method MassSpectrum MassSpectrum-class totalIonCurrent totalIonCurrent,MassSpectrum-method |
| Relaxed Value Matching | match.closest |
| Merges 'MassPeaks' objects. | mergeMassPeaks |
| Finds monoisotopic peaks in a MassPeaks object. | monoisotopicPeaks monoisotopicPeaks,list-method monoisotopicPeaks,MassPeaks-method |
| Turn a list of AbstractMassObjects into a mass spectrometry imaging slice. | msiSlices |
| Plots an AbstractMassObject object. | plot,AbstractMassObject,missing-method plot,MassSpectrum,missing-method |
| Plots a Mass Spectrometry Imaging dataset. | plotMsiSlice plotMsiSlice,array-method plotMsiSlice,list-method plotMsiSlice,matrix-method |
| Creates a reference 'MassPeaks' object. | referencePeaks |
| Removes the baseline of a MassSpectrum object. | removeBaseline removeBaseline,list-method removeBaseline,MassSpectrum-method |
| Smoothes intensities of a MassSpectrum object. | smoothIntensity smoothIntensity,list-method smoothIntensity,MassSpectrum-method |
| Transforms intensities of an AbstractMassObject object. | transformIntensity transformIntensity,AbstractMassObject-method transformIntensity,list-method |
| Trim an AbstractMassObject object. | trim trim,AbstractMassObject,numeric-method trim,list,missing-method trim,list,numeric-method |
| Run warping functions on AbstractMassObject objects. | warpMassPeaks warpMassSpectra |
