# Quantitative Analysis of Mass Spectrometry Data

## Documentation for package ‘MALDIquant’ version 1.22

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

MALDIquant-package | Quantitative Analysis of Mass Spectrometry Data
AbstractMassObject-class | Class "AbstractMassObject"
alignSpectra | Align MassSpectrum objects.
as.matrix-method | Class "AbstractMassObject"
averageMassSpectra | Averages 'MassSpectrum' objects.
binPeaks | Align Peaks into discrete bins.
calibrateIntensity | Calibrates intensities of a MassSpectrum object.
calibrateIntensity-method | Calibrates intensities of a MassSpectrum object.
coordinates | Class "AbstractMassObject"
coordinates-method | Class "AbstractMassObject"
coordinates<- | Class "AbstractMassObject"
coordinates<--method | Class "AbstractMassObject"
createMassPeaks | Creates a MassPeaks object.
createMassSpectrum | Creates a MassSpectrum object.
detectPeaks | Detects peaks in a MassSpectrum object.
detectPeaks-method | Detects peaks in a MassSpectrum object.
determineWarpingFunctions | Determine warping functions of MassPeaks objects.
estimateBaseline | Estimates the baseline of a MassSpectrum object.
estimateBaseline-method | Estimates the baseline of a MassSpectrum object.
estimateNoise | Estimates the noise of a MassSpectrum object.
estimateNoise-method | Estimates the noise of a MassSpectrum object.
fiedler2009subset | Example Mass Spectra (raw)
filterPeaks | Removes less frequent peaks.
findEmptyMassObjects | Finds or removes empty AbstractMassObject objects in a list.
intensity | Class "AbstractMassObject"
intensity-method | Class "AbstractMassObject"
intensity<- | Class "AbstractMassObject"
intensity<--method | Class "AbstractMassObject"
intensityMatrix | Converts a list of MassPeaks objects into a matrix.
isEmpty | Class "AbstractMassObject"
isEmpty-method | Class "AbstractMassObject"
isMassPeaks | Tests for MassSpectrum or MassPeaks object.
isMassPeaksList | Tests a list of MassSpectrum or MassPeaks objects.
isMassSpectrum | Tests for MassSpectrum or MassPeaks object.
isMassSpectrumList | Tests a list of MassSpectrum or MassPeaks objects.
isRegular | Class "MassSpectrum"
isRegular-method | Class "MassSpectrum"
labelPeaks | Draws peak labels to plot.
labelPeaks-method | Draws peak labels to plot.
length-method | Class "AbstractMassObject"
lines-method | Class "AbstractMassObject"
MALDIquant | Quantitative Analysis of Mass Spectrometry Data
MALDIquant-parallel | Parallel Support in Package 'MALDIquant'
mass | Class "AbstractMassObject"
mass-method | Class "AbstractMassObject"
mass<- | Class "AbstractMassObject"
mass<--method | Class "AbstractMassObject"
MassPeaks | Class "MassPeaks"
MassPeaks-class | Class "MassPeaks"
MassSpectrum | Class "MassSpectrum"
MassSpectrum-class | Class "MassSpectrum"
match.closest | Relaxed Value Matching
mergeMassPeaks | Merges 'MassPeaks' objects.
metaData | Class "AbstractMassObject"
metaData-method | Class "AbstractMassObject"
metaData<- | Class "AbstractMassObject"
metaData<--method | Class "AbstractMassObject"
monoisotopicPeaks | Finds monoisotopic peaks in a MassPeaks object.
monoisotopicPeaks-method | Finds monoisotopic peaks in a MassPeaks object.
msiSlices | Turn a list of AbstractMassObjects into a mass spectrometry imaging slice.
mz | Class "AbstractMassObject"
mz-method | Class "AbstractMassObject"
mz<- | Class "AbstractMassObject"
mz<--method | Class "AbstractMassObject"
plot-method | Plots an AbstractMassObject object.
plotMsiSlice | Plots a Mass Spectrometry Imaging dataset.
plotMsiSlice-method | Plots a Mass Spectrometry Imaging dataset.
points-method | Class "AbstractMassObject"
referencePeaks | Creates a reference 'MassPeaks' object.
removeBaseline | Removes the baseline of a MassSpectrum object.
removeBaseline-method | Removes the baseline of a MassSpectrum object.
removeEmptyMassObjects | Finds or removes empty AbstractMassObject objects in a list.
smoothIntensity | Smoothes intensities of a MassSpectrum object.
smoothIntensity-method | Smoothes intensities of a MassSpectrum object.
snr | Class "MassPeaks"
snr-method | Class "MassPeaks"
totalIonCurrent | Class "MassSpectrum"
totalIonCurrent-method | Class "MassSpectrum"
transformIntensity | Transforms intensities of an AbstractMassObject object.
transformIntensity-method | Transforms intensities of an AbstractMassObject object.
trim | Trim an AbstractMassObject object.
trim-method | Trim an AbstractMassObject object.
warpMassPeaks | Run warping functions on AbstractMassObject objects.
warpMassSpectra | Run warping functions on AbstractMassObject objects.
[-method | Class "AbstractMassObject"