tofsims-package	tofsims-package
addFixedWidth	addFixedWidth
addFixedWidth,PeakList,numeric,numeric-method	addFixedWidth
addPeaks	addPeaks
addPeaks,PeakList,missing,numeric-method	addPeaks
addPeaks,PeakList,numeric,numeric-method	addPeaks
analysis	analysis
analysis,MassSpectra,missing-method	analysis
analysis,MassSpectra,numeric-method	analysis
analysis<-	analysis
analysis<-,MassSpectra-method	analysis
analysisName	analysisName
analysisName,MassSpectra-method	analysisName
analysisName<-	analysisName
analysisName<-,MassSpectra-method	analysisName
baseObject	baseObject
baseObject,PrComp-method	baseObject-PrComp-method
baseObject,PrinComp-method	baseObject-PrinComp-method
binning	binning
binning,MassImage-method	binning
bwApply	bwApply
bwApply,MassSpectra,matrix-method	bwApply
calibPointNew	calibPointNew
calibPointNew,MassSpectra,numeric-method	calibPointNew
calibPoints	calibPoints
calibPoints,MassSpectra-method	calibPoints
calibPoints<-	calibPoints
calibPoints<-,MassSpectra-method	calibPoints
calibration	calibration
calibration,MassSpectra-method	calibration
calibration<-	calibration
calibration<-,MassSpectra-method	calibration
changePeakWidth	changePeakWidth
changePeakWidth,PeakList,missing,missing,missing-method	changePeakWidth
changePeakWidth,PeakList,numeric,numeric,numeric-method	changePeakWidth
check.extension	check.extension
computeMNF	computeMNF
computeNoise	computeNoise
coordToPixel	coordToPixel
coordToPixel,MassImage,numeric-method	coordToPixel-MassImage-numeric-method
covDiffCalc	covDiffCalc
cReadRawPhi	cReadRawPhi
cTable	ctable
ctable	ctable
dim,MassImage-method	dim-MassImage-method
dim,MassSpectra-method	dim-MassSpectra-method
EigenDecompose	EigenDecompose
extract.header.data	extract.header.data
findClosestMatch	findClosestMatch
findPeakWidth	findPeakWidth
findPeakWidth,PeakList-method	findPeakWidth
getTOFs	getTOFs
getTOFs,MassSpectra-method	getTOFs
image	image
image,MassImage-method	image
image,PCA-method	image
imageMatrix	imageMatrix
imageMatrix,MassImage-method	imageMatrix
imageMatrix,PCA-method	imageMatrix
import	import
import.raw	import.raw
instrument	instrument
instrument,MassSpectra-method	instrument
instrument<-	instrument
instrument<-,MassSpectra-method	instrument
iters	iters
iters,MCR-method	iters-MCR-method
itzipName	itzipName
itzipName<-	itzipName-set
LapackGenEigen	LapackGenEigen
legend.col	legend.col
look.for.itzip.property	look.for.itzip.property
MAF	MAF
makeTIC	makeTIC
makeTIC,MassSpectra-method	makeTIC-MassSpectra-method
manualSelectPeaks	manualSelectPeaks
MassImage	MassImage
MassSpectra	MassSpectra
MCR	MCR
MCR-class	MCR
MNF	MNF
mz,MassSpectra-method	mz
mz<-,MassSpectra-method	mz
nComp	nComp
nComp,PCA-method	nComp
ndim	ndim
ndim,MassSpectra-method	ndim-MassSpectra-method
nearestNeighbourMean	nearestNeighbourMean
nnMean	nnMean
nnMNF	nnMNF
noPlottingData	noPlottingData
noPlottingData,PCA-method	noPlottingData-PCA-method
nPeaks	nPeaks
nPeaks,PeakList-method	nPeaks
nz	nz
nz,MassSpectra,missing-method	nz
nz,MassSpectra,numeric-method	nz
nz<-	nz
nz<-,MassSpectra-method	nz
opaMCR	MCR
overlayPlot	overlayPlot
overlayPlot,list-method	overlayPlot
parIndicesSearch	parIndicesSearch
PCA	PCA-class
PCA-class	PCA-class
pcaLoadings	pcaLoadings
pcaLoadings,PCA,missing-method	pcaLoadings
pcaLoadings,PCA,numeric-method	pcaLoadings
pcaMAF	pcaMAF
PCAnalysis	PCAnalysis
pcaScores	pcaScores
pcaScores,PCA,ANY-method	pcaScores
pcaScores,PCA,numeric-method	pcaScores
peakIDs	peakIDs
peakIDs,PeakList-method	peakIDs
peakIDs<-	peakIDs
peakIDs<-,PeakList-method	peakIDs
PeakList	PeakList
peakMzs	peakMzs
peakMzs,PeakList-method	peakMzs
peakMzs<-	peakMzs
peakMzs<-,PeakList-method	peakMzs
peakPick	peakPick
peakPick,MassSpectra-method	peakPick
peaks2Spectra	peaks2Spectra
peaks2Spectra,PeakList,MassSpectra-method	peaks2Spectra
peakWidths	peakWidths
peakWidths,PeakList-method	peakWidths
plot	plot
plot,MassImage,missing-method	plot-MassImage-missing-method
plot,MassSpectra,missing-method	plot
plot,PCA,ANY-method	plot
plot,PeakList,missing-method	plot-PeakList-missing-method
points	points
points,MassSpectra-method	points
poissonScaling	poissonScaling
poissonScaling,MassSpectra-method	poissonScaling
PrComp	PrComp
prComp	PrComp
PrComp-class	PrComp
PrinComp	PrinComp
prinComp	PrinComp
PrinComp-class	PrinComp
readBIF	readBIF
recalibrate	recalibrate
recalibrate,MassSpectra-method	recalibrate
reduceSpectrumResolution	reduceSpectrumResolution
reduceSpectrumResolution,MassSpectra-method	reduceSpectrumResolution
removePeaks	removePeaks
removePeaks,PeakList,missing,character,numeric,missing-method	removePeaks
removePeaks,PeakList,missing,missing,missing,numeric-method	removePeaks
removePeaks,PeakList,missing,missing,numeric,missing-method	removePeaks
removePeaks,PeakList,numeric,missing,missing,missing-method	removePeaks
resids	resids
resids,MCR-method	resids-MCR-method
RSS	RSS
RSS,MCR-method	RSS-MCR-method
scale	scale
scale,MassSpectra-method	scale
show,MassImage-method	show-MassImage-method
show,MassSpectra-method	show-MassSpectra-method
show,PeakList-method	show-PeakList-method
smootherGolay	smootherGolay
smootherGolay,MassSpectra-method	smootherGolay
smootherSpline	smootherSpline
smootherSpline,MassSpectra-method	smootherSpline
smoothScatter	smoothScatter
smoothScatter,PCA-method	smoothScatter
SNR	SNR
subset	subset
subset,MassImage-method	subset
unitMassPeaks	unitMassPeaks
unitMassPeaks,MassSpectra,numeric,numeric-method	unitMassPeaks
validMassImageObject	validMassImageObject
validMassSpectraObject	validMassSpectraObject
validPCAObject	validPCAObject
validPeakListObject	validPeakListObject
xdim	xdim
xdim,MassImage-method	xdim-MassImage-method
xdim,PCA-method	xdim-PCA-method
xdim<-	xdim-set
xy	xy
xy,MassImage-method	xy
xy<-	xy
xy<-,MassImage-method	xy
xySpec	xySpec
xySpec,MassImage-method	xySpec
ydim	ydim
ydim,MassImage-method	ydim-MassImage-method
ydim,PCA-method	ydim-PCA-method
ydim<-	ydim-set
zdim	zdim
zdim,MassSpectra-method	zdim-MassSpectra-method
