MALDIquant-package	MALDIquant-package
AbstractMassObject-class	AbstractMassObject-class
alignSpectra	alignSpectra-functions
as.matrix,AbstractMassObject-method	AbstractMassObject-class
averageMassSpectra	averageMassSpectra-functions
binPeaks	binPeaks-functions
calibrateIntensity	calibrateIntensity-methods
calibrateIntensity,list-method	calibrateIntensity-methods
calibrateIntensity,MassSpectrum-method	calibrateIntensity-methods
coordinates	AbstractMassObject-class
coordinates,AbstractMassObject-method	AbstractMassObject-class
coordinates,list-method	AbstractMassObject-class
coordinates<-	AbstractMassObject-class
coordinates<-,AbstractMassObject,matrix-method	AbstractMassObject-class
coordinates<-,AbstractMassObject,numeric-method	AbstractMassObject-class
coordinates<-,list,matrix-method	AbstractMassObject-class
createMassPeaks	createMassPeaks-functions
createMassSpectrum	createMassSpectrum-functions
detectPeaks	detectPeaks-methods
detectPeaks,list-method	detectPeaks-methods
detectPeaks,MassSpectrum-method	detectPeaks-methods
determineWarpingFunctions	determineWarpingFunctions-functions
estimateBaseline	estimateBaseline-methods
estimateBaseline,MassSpectrum-method	estimateBaseline-methods
estimateNoise	estimateNoise-methods
estimateNoise,MassSpectrum-method	estimateNoise-methods
fiedler2009subset	fiedler2009subset
filterPeaks	filterPeaks-functions
findEmptyMassObjects	findEmptyMassObjects-functions
intensity	AbstractMassObject-class
intensity,AbstractMassObject-method	AbstractMassObject-class
intensity<-	AbstractMassObject-class
intensity<-,AbstractMassObject,numeric-method	AbstractMassObject-class
intensityMatrix	intensityMatrix-functions
isEmpty	AbstractMassObject-class
isEmpty,AbstractMassObject-method	AbstractMassObject-class
isMassPeaks	isMassObject-functions
isMassPeaksList	isMassObjectList-functions
isMassSpectrum	isMassObject-functions
isMassSpectrumList	isMassObjectList-functions
isRegular	MassSpectrum-class
isRegular,MassSpectrum-method	MassSpectrum-class
labelPeaks	labelPeaks-methods
labelPeaks,MassPeaks-method	labelPeaks-methods
length,AbstractMassObject-method	AbstractMassObject-class
lines,AbstractMassObject-method	AbstractMassObject-class
MALDIquant	MALDIquant-package
MALDIquant-defunct	MALDIquant-defunct
MALDIquant-deprecated	MALDIquant-deprecated
MALDIquant-parallel	MALDIquant-parallel
mass	AbstractMassObject-class
mass,AbstractMassObject-method	AbstractMassObject-class
mass<-	AbstractMassObject-class
mass<-,AbstractMassObject,numeric-method	AbstractMassObject-class
MassPeaks	MassPeaks-class
MassPeaks-class	MassPeaks-class
MassSpectrum	MassSpectrum-class
MassSpectrum-class	MassSpectrum-class
match.closest	match.closest
mergeMassPeaks	mergeMassPeaks-functions
metaData	AbstractMassObject-class
metaData,AbstractMassObject-method	AbstractMassObject-class
metaData<-	AbstractMassObject-class
metaData<-,AbstractMassObject-method	AbstractMassObject-class
monoisotopicPeaks	monoisotopicPeaks-methods
monoisotopicPeaks,list-method	monoisotopicPeaks-methods
monoisotopicPeaks,MassPeaks-method	monoisotopicPeaks-methods
msiSlices	msiSlices-functions
mz	AbstractMassObject-class
mz,AbstractMassObject-method	AbstractMassObject-class
mz<-	AbstractMassObject-class
mz<-,AbstractMassObject,numeric-method	AbstractMassObject-class
plot,AbstractMassObject,missing-method	plot-methods
plot,MassSpectrum,missing-method	plot-methods
plotMsiSlice	plotMsiSlice-methods
plotMsiSlice,array-method	plotMsiSlice-methods
plotMsiSlice,list-method	plotMsiSlice-methods
plotMsiSlice,matrix-method	plotMsiSlice-methods
points,AbstractMassObject-method	AbstractMassObject-class
referencePeaks	referencePeaks-functions
removeBaseline	removeBaseline-methods
removeBaseline,list-method	removeBaseline-methods
removeBaseline,MassSpectrum-method	removeBaseline-methods
removeEmptyMassObjects	findEmptyMassObjects-functions
smoothIntensity	smoothIntensity-methods
smoothIntensity,list-method	smoothIntensity-methods
smoothIntensity,MassSpectrum-method	smoothIntensity-methods
snr	MassPeaks-class
snr,MassPeaks-method	MassPeaks-class
totalIonCurrent	MassSpectrum-class
totalIonCurrent,MassSpectrum-method	MassSpectrum-class
transformIntensity	transformIntensity-methods
transformIntensity,AbstractMassObject-method	transformIntensity-methods
transformIntensity,list-method	transformIntensity-methods
trim	trim-methods
trim,AbstractMassObject,numeric-method	trim-methods
trim,list,missing-method	trim-methods
trim,list,numeric-method	trim-methods
warpMassPeaks	warp-functions
warpMassSpectra	warp-functions
[,AbstractMassObject,logical,missing-method	AbstractMassObject-class
[,AbstractMassObject,numeric,missing-method	AbstractMassObject-class
[,MassPeaks,logical,missing-method	AbstractMassObject-class
[,MassPeaks,numeric,missing-method	AbstractMassObject-class
