Quantitative Analysis of Mass Spectrometry Data

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Documentation for package ‘MALDIquant’ version 1.22.2

• 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"