Cardinal-package	Cardinal-package
$,iSet-method	iSet-class
$,ResultSet-method	ResultSet-class
$<-,iSet-method	iSet-class
abstract,MIAPE-Imaging-method	MIAPE-Imaging-class
alpha.colors	colors-functions
annotatedDataFrameFrom,ImageData-method	ImageData-class
baselineReduction	MSImageProcess-class
baselineReduction,MSImageProcess-method	MSImageProcess-class
baselineReduction<-	MSImageProcess-class
baselineReduction<-,MSImageProcess-method	MSImageProcess-class
batchProcess	batchProcess-methods
batchProcess,MSImageSet-method	batchProcess-methods
batchProcess-methods	batchProcess-methods
Binmat	Binmat-class
Binmat-class	Binmat-class
Cardinal	Cardinal-package
cbind,Binmat-method	Binmat-class
cbind,Hashmat-method	Hashmat-class
centroided	MSImageProcess-class
centroided,MSImageProcess-method	MSImageProcess-class
centroided,MSImageSet-method	MSImageSet-class
centroided<-	MSImageProcess-class
centroided<-,MSImageProcess-method	MSImageProcess-class
centroided<-,MSImageSet-method	MSImageSet-class
class:Binmat	Binmat-class
class:Hashmat	Hashmat-class
class:IAnnotatedDataFrame	IAnnotatedDataFrame-class
class:ImageData	ImageData-class
class:iSet	iSet-class
class:MIAPE-Imaging	MIAPE-Imaging-class
class:MSImageData	MSImageData-class
class:MSImageProcess	MSImageProcess-class
class:MSImageSet	MSImageSet-class
class:OPLS	OPLS-methods
class:PCA	PCA-methods
class:PLS	PLS-methods
class:ResultSet	ResultSet-class
class:SImageData	SImageData-class
class:SImageSet	SImageSet-class
class:SpatialKMeans	spatialKMeans-methods
class:SpatialShrunkenCentroids	spatialShrunkenCentroids-methods
colnames,Binmat-method	Binmat-class
colnames,Hashmat-method	Hashmat-class
colnames<-,Binmat-method	Binmat-class
colnames<-,Hashmat-method	Hashmat-class
combine,array,array-method	ImageData-class
combine,Hashmat,Hashmat-method	Hashmat-class
combine,IAnnotatedDataFrame,IAnnotatedDataFrame-method	IAnnotatedDataFrame-class
combine,ImageData,ImageData-method	ImageData-class
combine,iSet,iSet-method	iSet-class
combine,MIAPE-Imaging,MIAPE-Imaging-method	MIAPE-Imaging-class
combine,MSImageProcess,MSImageProcess-method	MSImageProcess-class
combine,MSImageSet,MSImageSet-method	MSImageSet-class
combine,SImageData,SImageData-method	SImageData-class
combine,SImageSet,SImageSet-method	SImageSet-class
coord	coord-methods
coord,IAnnotatedDataFrame-method	IAnnotatedDataFrame-class
coord,iSet-method	iSet-class
coord,SImageData-method	SImageData-class
coord-methods	coord-methods
coord<-	coord-methods
coord<-,IAnnotatedDataFrame-method	IAnnotatedDataFrame-class
coord<-,iSet-method	iSet-class
coord<-,SImageData-method	SImageData-class
coord<-,SImageSet-method	SImageSet-class
coordinates	coord-methods
coordinates-methods	coord-methods
coordinates<-	coord-methods
coordLabels	coord-methods
coordLabels,IAnnotatedDataFrame-method	IAnnotatedDataFrame-class
coordLabels,iSet-method	iSet-class
coordLabels-methods	coord-methods
coordLabels<-	coord-methods
coordLabels<-,IAnnotatedDataFrame-method	IAnnotatedDataFrame-class
coordLabels<-,iSet-method	iSet-class
coordLabels<-,SImageSet-method	SImageSet-class
coregister	coregister-methods
coregister,SpatialKMeans,missing-method	coregister-methods
coregister,SpatialShrunkenCentroids,missing-method	coregister-methods
coregister-methods	coregister-methods
cvApply	cvApply-methods
cvApply,SImageSet-method	cvApply-methods
cvApply-methods	cvApply-methods
dim,Binmat-method	Binmat-class
dim,Hashmat-method	Hashmat-class
dim,ImageData-method	ImageData-class
dim,iSet-method	iSet-class
dim,SImageData-method	SImageData-class
dim<-,Binmat-method	Binmat-class
dim<-,Hashmat-method	Hashmat-class
dimnames,Binmat-method	Binmat-class
dimnames,Hashmat-method	Hashmat-class
dimnames<-,Binmat,ANY-method	Binmat-class
dimnames<-,Binmat-method	Binmat-class
dimnames<-,Hashmat,ANY-method	Hashmat-class
dimnames<-,Hashmat-method	Hashmat-class
dims,ImageData-method	ImageData-class
dims,iSet-method	iSet-class
dims,SImageData-method	SImageData-class
embeddingMethod	MIAPE-Imaging-class
embeddingMethod,MIAPE-Imaging-method	MIAPE-Imaging-class
embeddingMethod<-	MIAPE-Imaging-class
embeddingMethod<-,MIAPE-Imaging-method	MIAPE-Imaging-class
experimentData,iSet-method	iSet-class
experimentData<-,iSet-method	iSet-class
expinfo,MIAPE-Imaging-method	MIAPE-Imaging-class
fData,iSet-method	iSet-class
fData<-,iSet,ANY-method	iSet-class
fData<-,iSet-method	iSet-class
featureApply	pixelApply-methods
featureApply,SImageSet-method	pixelApply-methods
featureApply-methods	pixelApply-methods
featureData,iSet-method	iSet-class
featureData<-,iSet,ANY-method	iSet-class
featureData<-,iSet-method	iSet-class
featureNames,iSet-method	iSet-class
featureNames,SImageData-method	SImageData-class
featureNames<-,iSet-method	iSet-class
featureNames<-,SImageData-method	SImageData-class
featureNames<-,SImageSet-method	SImageSet-class
features	pixels-methods
features,iSet-method	pixels-methods
features,MSImageSet-method	pixels-methods
features-methods	pixels-methods
files	MSImageProcess-class
files,MSImageProcess-method	MSImageProcess-class
files<-	MSImageProcess-class
files<-,MSImageProcess-method	MSImageProcess-class
fvarLabels,iSet-method	iSet-class
fvarLabels<-,iSet-method	iSet-class
fvarMetadata,iSet-method	iSet-class
fvarMetadata<-,iSet,ANY-method	iSet-class
fvarMetadata<-,iSet-method	iSet-class
generateImage	generateImage
generateSpectrum	generateSpectrum
gradient.colors	colors-functions
Hashmat	Hashmat-class
Hashmat-class	Hashmat-class
IAnnotatedDataFrame	IAnnotatedDataFrame-class
IAnnotatedDataFrame-class	IAnnotatedDataFrame-class
iData	imageData-methods
iData,iSet-method	iSet-class
iData,SImageData-method	SImageData-class
iData,SImageSet-method	SImageSet-class
iData-methods	imageData-methods
iData<-	imageData-methods
iData<-,iSet-method	iSet-class
iData<-,SImageData-method	SImageData-class
iData<-,SImageSet-method	SImageSet-class
image	image-methods
image,CrossValidated-method	image-methods
image,MSImageSet-method	image-methods
image,OPLS-method	image-methods
image,PCA-method	image-methods
image,PLS-method	image-methods
image,ResultSet-method	image-methods
image,SImageSet-method	image-methods
image,SpatialKMeans-method	image-methods
image,SpatialShrunkenCentroids-method	image-methods
image-methods	image-methods
image3D	image-methods
image3D,CrossValidated-method	image-methods
image3D,MSImageSet-method	image-methods
image3D,OPLS-method	image-methods
image3D,PCA-method	image-methods
image3D,PLS-method	image-methods
image3D,ResultSet-method	image-methods
image3D,SImageSet-method	image-methods
image3D,SpatialKMeans-method	image-methods
image3D,SpatialShrunkenCentroids-method	image-methods
image3D-methods	image-methods
ImageData	ImageData-class
imageData	imageData-methods
imageData,iSet-method	iSet-class
ImageData-class	ImageData-class
imageData-methods	imageData-methods
imageData<-	imageData-methods
imageData<-,iSet-method	iSet-class
imageShape	MIAPE-Imaging-class
imageShape,MIAPE-Imaging-method	MIAPE-Imaging-class
imageShape<-	MIAPE-Imaging-class
imageShape<-,MIAPE-Imaging-method	MIAPE-Imaging-class
initialize,Binmat-method	Binmat-class
initialize,Hashmat-method	Hashmat-class
initialize,IAnnotatedDataFrame-method	IAnnotatedDataFrame-class
initialize,ImageData-method	ImageData-class
initialize,iSet-method	iSet-class
initialize,MSImageData-method	MSImageData-class
initialize,MSImageProcess-method	MSImageProcess-class
initialize,MSImageSet-method	MSImageSet-class
initialize,SImageData-method	SImageData-class
initialize,SImageSet-method	SImageSet-class
inSituChemistry	MIAPE-Imaging-class
inSituChemistry,MIAPE-Imaging-method	MIAPE-Imaging-class
inSituChemistry<-	MIAPE-Imaging-class
inSituChemistry<-,MIAPE-Imaging-method	MIAPE-Imaging-class
instrumentModel	MIAPE-Imaging-class
instrumentModel,MIAPE-Imaging-method	MIAPE-Imaging-class
instrumentModel<-	MIAPE-Imaging-class
instrumentModel<-,MIAPE-Imaging-method	MIAPE-Imaging-class
instrumentVendor	MIAPE-Imaging-class
instrumentVendor,MIAPE-Imaging-method	MIAPE-Imaging-class
instrumentVendor<-	MIAPE-Imaging-class
instrumentVendor<-,MIAPE-Imaging-method	MIAPE-Imaging-class
intensity.colors	colors-functions
ionizationType	MIAPE-Imaging-class
ionizationType,MIAPE-Imaging-method	MIAPE-Imaging-class
ionizationType<-	MIAPE-Imaging-class
ionizationType<-,MIAPE-Imaging-method	MIAPE-Imaging-class
iSet	iSet-class
iSet-class	iSet-class
keys	Hashmat-class
keys,Hashmat-method	Hashmat-class
keys<-	Hashmat-class
keys<-,Hashmat,character-method	Hashmat-class
keys<-,Hashmat,list-method	Hashmat-class
keys<-,Hashmat-method	Hashmat-class
length,ResultSet-method	ResultSet-class
lineScanDirection	MIAPE-Imaging-class
lineScanDirection,MIAPE-Imaging-method	MIAPE-Imaging-class
lineScanDirection<-	MIAPE-Imaging-class
lineScanDirection<-,MIAPE-Imaging-method	MIAPE-Imaging-class
logLik,SpatialShrunkenCentroids-method	spatialShrunkenCentroids-methods
massAnalyzerType	MIAPE-Imaging-class
massAnalyzerType,MIAPE-Imaging-method	MIAPE-Imaging-class
massAnalyzerType<-	MIAPE-Imaging-class
massAnalyzerType<-,MIAPE-Imaging-method	MIAPE-Imaging-class
matrixApplication	MIAPE-Imaging-class
matrixApplication,MIAPE-Imaging-method	MIAPE-Imaging-class
matrixApplication<-	MIAPE-Imaging-class
matrixApplication<-,MIAPE-Imaging-method	MIAPE-Imaging-class
MIAPE-Imaging	MIAPE-Imaging-class
MIAPE-Imaging-class	MIAPE-Imaging-class
modelData	ResultSet-class
modelData,ResultSet-method	ResultSet-class
modelData<-	ResultSet-class
modelData<-,ResultSet-method	ResultSet-class
msiInfo	MIAPE-Imaging-class
msiInfo,MIAPE-Imaging-method	MIAPE-Imaging-class
MSImageData	MSImageData-class
MSImageData-class	MSImageData-class
MSImageProcess	MSImageProcess-class
MSImageProcess-class	MSImageProcess-class
MSImageSet	MSImageSet-class
MSImageSet-class	MSImageSet-class
mz	mz-methods
mz,MSImageSet-method	MSImageSet-class
mz-methods	mz-methods
mz<-	mz-methods
mz<-,MSImageSet-method	MSImageSet-class
mzData	imageData-methods
mzData,MSImageData-method	MSImageData-class
mzData,SImageData-method	SImageData-class
mzData-methods	imageData-methods
mzData<-	imageData-methods
mzData<-,MSImageData-method	MSImageData-class
mzData<-,SImageData-method	SImageData-class
names,ImageData-method	ImageData-class
names,ResultSet-method	ResultSet-class
names<-,ImageData-method	ImageData-class
normalization	MSImageProcess-class
normalization,MSImageProcess-method	MSImageProcess-class
normalization<-	MSImageProcess-class
normalization<-,MSImageProcess-method	MSImageProcess-class
normalize	normalize-methods
normalize,MSImageSet-method	normalize-methods
normalize-methods	normalize-methods
normalize.tic	normalize-methods
notes,MIAPE-Imaging-method	MIAPE-Imaging-class
notes<-,MIAPE-Imaging-method	MIAPE-Imaging-class
OPLS	OPLS-methods
OPLS,SImageSet,character-method	OPLS-methods
OPLS,SImageSet,factor-method	OPLS-methods
OPLS,SImageSet,matrix-method	OPLS-methods
OPLS,SImageSet,numeric-method	OPLS-methods
OPLS-class	OPLS-methods
OPLS-methods	OPLS-methods
otherInfo,MIAPE-Imaging-method	MIAPE-Imaging-class
PCA	PCA-methods
PCA,SImageSet-method	PCA-methods
PCA-class	PCA-methods
PCA-methods	PCA-methods
pData	pixelData-methods
pData,Hashmat-method	Hashmat-class
pData,iSet-method	iSet-class
pData-methods	pixelData-methods
pData<-	pixelData-methods
pData<-,Hashmat,ANY-method	Hashmat-class
pData<-,Hashmat-method	Hashmat-class
pData<-,iSet,ANY-method	iSet-class
pData<-,iSet-method	iSet-class
peakAlign	peakAlign-methods
peakAlign,MSImageSet,missing-method	peakAlign-methods
peakAlign,MSImageSet,MSImageSet-method	peakAlign-methods
peakAlign,MSImageSet,numeric-method	peakAlign-methods
peakAlign-methods	peakAlign-methods
peakAlign.diff	peakAlign-methods
peakAlign.DP	peakAlign-methods
peakData	imageData-methods
peakData,MSImageData-method	MSImageData-class
peakData,SImageData-method	SImageData-class
peakData-methods	imageData-methods
peakData<-	imageData-methods
peakData<-,MSImageData-method	MSImageData-class
peakData<-,SImageData-method	SImageData-class
peakFilter	peakFilter-methods
peakFilter,MSImageSet-method	peakFilter-methods
peakFilter-methods	peakFilter-methods
peakFilter.freq	peakFilter-methods
peakPick	peakPick-methods
peakPick,MSImageSet-method	peakPick-methods
peakPick-methods	peakPick-methods
peakPick.adaptive	peakPick-methods
peakPick.limpic	peakPick-methods
peakPick.simple	peakPick-methods
peakPicking	MSImageProcess-class
peakPicking,MSImageProcess-method	MSImageProcess-class
peakPicking<-	MSImageProcess-class
peakPicking<-,MSImageProcess-method	MSImageProcess-class
peaks	imageData-methods
peaks,MSImageSet-method	MSImageSet-class
peaks-methods	imageData-methods
peaks<-	imageData-methods
peaks<-,MSImageSet-method	MSImageSet-class
pixelApply	pixelApply-methods
pixelApply,SImageSet-method	pixelApply-methods
pixelApply-methods	pixelApply-methods
pixelData	pixelData-methods
pixelData,iSet-method	iSet-class
pixelData-methods	pixelData-methods
pixelData<-	pixelData-methods
pixelData<-,iSet-method	iSet-class
pixelNames	pixelNames-methods
pixelNames,IAnnotatedDataFrame-method	IAnnotatedDataFrame-class
pixelNames,iSet-method	iSet-class
pixelNames,SImageData-method	SImageData-class
pixelNames-methods	pixelNames-methods
pixelNames<-	pixelNames-methods
pixelNames<-,IAnnotatedDataFrame-method	IAnnotatedDataFrame-class
pixelNames<-,iSet-method	iSet-class
pixelNames<-,SImageData-method	SImageData-class
pixelNames<-,SImageSet-method	SImageSet-class
pixels	pixels-methods
pixels,iSet-method	pixels-methods
pixels,MSImageSet-method	pixels-methods
pixels-methods	pixels-methods
pixelSize	MIAPE-Imaging-class
pixelSize,MIAPE-Imaging-method	MIAPE-Imaging-class
pixelSize<-	MIAPE-Imaging-class
pixelSize<-,MIAPE-Imaging-method	MIAPE-Imaging-class
plot	plot-methods
plot,CrossValidated,missing-method	plot-methods
plot,MSImageSet,formula-method	plot-methods
plot,MSImageSet,missing-method	plot-methods
plot,OPLS,missing-method	plot-methods
plot,PCA,missing-method	plot-methods
plot,PLS,missing-method	plot-methods
plot,ResultSet,formula-method	plot-methods
plot,ResultSet,missing-method	plot-methods
plot,SImageSet,formula-method	plot-methods
plot,SImageSet,missing-method	plot-methods
plot,SpatialKMeans,missing-method	plot-methods
plot,SpatialShrunkenCentroids,missing-method	plot-methods
plot-methods	plot-methods
plot.summary.CrossValidated	cvApply-methods
plot.summary.OPLS	OPLS-methods
plot.summary.PCA	PCA-methods
plot.summary.PLS	PLS-methods
plot.summary.SpatialKMeans	spatialKMeans-methods
plot.summary.SpatialShrunkenCentroids	spatialShrunkenCentroids-methods
PLS	PLS-methods
PLS,SImageSet,character-method	PLS-methods
PLS,SImageSet,factor-method	PLS-methods
PLS,SImageSet,matrix-method	PLS-methods
PLS,SImageSet,numeric-method	PLS-methods
PLS-class	PLS-methods
PLS-methods	PLS-methods
positionArray	SImageData-class
positionArray,SImageData-method	SImageData-class
positionArray<-	SImageData-class
positionArray<-,SImageData-method	SImageData-class
predict,OPLS-method	OPLS-methods
predict,PCA-method	PCA-methods
predict,PLS-method	PLS-methods
predict,SpatialShrunkenCentroids-method	spatialShrunkenCentroids-methods
print.summary.CrossValidated	cvApply-methods
print.summary.iSet	iSet-class
print.summary.OPLS	OPLS-methods
print.summary.PCA	PCA-methods
print.summary.PLS	PLS-methods
print.summary.SpatialKMeans	spatialKMeans-methods
print.summary.SpatialShrunkenCentroids	spatialShrunkenCentroids-methods
processingData	processingData-methods
processingData,MSImageSet-method	MSImageSet-class
processingData-methods	processingData-methods
processingData<-	processingData-methods
processingData<-,MSImageSet-method	MSImageSet-class
prochistory	MSImageProcess-class
prochistory,MSImageProcess-method	MSImageProcess-class
prochistory<-	MSImageProcess-class
prochistory<-,MSImageProcess,character-method	MSImageProcess-class
prochistory<-,MSImageProcess,list-method	MSImageProcess-class
prochistory<-,MSImageProcess-method	MSImageProcess-class
protocolData,iSet-method	iSet-class
protocolData<-,iSet-method	iSet-class
pubMedIds,MIAPE-Imaging-method	MIAPE-Imaging-class
pubMedIds<-,MIAPE-Imaging-method	MIAPE-Imaging-class
rbind,Binmat-method	Binmat-class
rbind,Hashmat-method	Hashmat-class
readAnalyze	readMSIData
readImzML	readMSIData
readMSIData	readMSIData
reduceBaseline	reduceBaseline-methods
reduceBaseline,MSImageSet-method	reduceBaseline-methods
reduceBaseline-methods	reduceBaseline-methods
reduceBaseline.median	reduceBaseline-methods
reduceDimension	reduceDimension-methods
reduceDimension,MSImageSet,missing-method	reduceDimension-methods
reduceDimension,MSImageSet,MSImageSet-method	reduceDimension-methods
reduceDimension,MSImageSet,numeric-method	reduceDimension-methods
reduceDimension-methods	reduceDimension-methods
reduceDimension.bin	reduceDimension-methods
reduceDimension.peaks	reduceDimension-methods
reduceDimension.resample	reduceDimension-methods
regeneratePositions	SImageData-class
regeneratePositions,SImageData-method	SImageData-class
regeneratePositions,SImageSet-method	SImageSet-class
resultData	ResultSet-class
resultData,ResultSet-method	ResultSet-class
resultData<-	ResultSet-class
resultData<-,ResultSet-method	ResultSet-class
ResultSet	ResultSet-class
ResultSet-class	ResultSet-class
risk.colors	colors-functions
rownames,Binmat-method	Binmat-class
rownames,Hashmat-method	Hashmat-class
rownames<-,Binmat-method	Binmat-class
rownames<-,Hashmat-method	Hashmat-class
sampleNames,IAnnotatedDataFrame-method	IAnnotatedDataFrame-class
sampleNames,iSet-method	iSet-class
sampleNames<-,IAnnotatedDataFrame,ANY-method	IAnnotatedDataFrame-class
sampleNames<-,IAnnotatedDataFrame-method	IAnnotatedDataFrame-class
sampleNames<-,iSet,ANY-method	iSet-class
sampleNames<-,iSet-method	iSet-class
samples,MIAPE-Imaging-method	MIAPE-Imaging-class
scanDirection	MIAPE-Imaging-class
scanDirection,MIAPE-Imaging-method	MIAPE-Imaging-class
scanDirection<-	MIAPE-Imaging-class
scanDirection<-,MIAPE-Imaging-method	MIAPE-Imaging-class
scanPattern	MIAPE-Imaging-class
scanPattern,MIAPE-Imaging-method	MIAPE-Imaging-class
scanPattern<-	MIAPE-Imaging-class
scanPattern<-,MIAPE-Imaging-method	MIAPE-Imaging-class
scanPolarity	MIAPE-Imaging-class
scanPolarity,MIAPE-Imaging-method	MIAPE-Imaging-class
scanPolarity<-	MIAPE-Imaging-class
scanPolarity<-,MIAPE-Imaging-method	MIAPE-Imaging-class
scanType	MIAPE-Imaging-class
scanType,MIAPE-Imaging-method	MIAPE-Imaging-class
scanType<-	MIAPE-Imaging-class
scanType<-,MIAPE-Imaging-method	MIAPE-Imaging-class
select	select-methods
select,SImageSet-method	select-methods
select-methods	select-methods
show,Binmat-method	Binmat-class
show,Hashmat-method	Hashmat-class
show,ImageData-method	ImageData-class
show,MIAPE-Imaging-method	MIAPE-Imaging-class
show,MSImageProcess-method	MSImageProcess-class
show,ResultSet-method	ResultSet-class
SImageData	SImageData-class
SImageData-class	SImageData-class
SImageSet	SImageSet-class
SImageSet-class	SImageSet-class
smoothing	MSImageProcess-class
smoothing,MSImageProcess-method	MSImageProcess-class
smoothing<-	MSImageProcess-class
smoothing<-,MSImageProcess-method	MSImageProcess-class
smoothSignal	smoothSignal-methods.R
smoothSignal,MSImageSet-method	smoothSignal-methods.R
smoothSignal-methods	smoothSignal-methods.R
smoothSignal.gaussian	smoothSignal-methods.R
smoothSignal.ma	smoothSignal-methods.R
smoothSignal.sgolay	smoothSignal-methods.R
softwareName	MIAPE-Imaging-class
softwareName,MIAPE-Imaging-method	MIAPE-Imaging-class
softwareName<-	MIAPE-Imaging-class
softwareName<-,MIAPE-Imaging-method	MIAPE-Imaging-class
softwareVersion	MIAPE-Imaging-class
softwareVersion,MIAPE-Imaging-method	MIAPE-Imaging-class
softwareVersion<-	MIAPE-Imaging-class
softwareVersion<-,MIAPE-Imaging-method	MIAPE-Imaging-class
spatialKMeans	spatialKMeans-methods
spatialKMeans,SImageSet-method	spatialKMeans-methods
SpatialKMeans-class	spatialKMeans-methods
spatialKMeans-methods	spatialKMeans-methods
spatialShrunkenCentroids	spatialShrunkenCentroids-methods
spatialShrunkenCentroids,SImageSet,character-method	spatialShrunkenCentroids-methods
spatialShrunkenCentroids,SImageSet,factor-method	spatialShrunkenCentroids-methods
spatialShrunkenCentroids,SImageSet,missing-method	spatialShrunkenCentroids-methods
SpatialShrunkenCentroids-class	spatialShrunkenCentroids-methods
spatialShrunkenCentroids-methods	spatialShrunkenCentroids-methods
specimenOrigin	MIAPE-Imaging-class
specimenOrigin,MIAPE-Imaging-method	MIAPE-Imaging-class
specimenOrigin<-	MIAPE-Imaging-class
specimenOrigin<-,MIAPE-Imaging-method	MIAPE-Imaging-class
specimenType	MIAPE-Imaging-class
specimenType,MIAPE-Imaging-method	MIAPE-Imaging-class
specimenType<-	MIAPE-Imaging-class
specimenType<-,MIAPE-Imaging-method	MIAPE-Imaging-class
spectra	imageData-methods
spectra,MSImageSet-method	MSImageSet-class
spectra-methods	imageData-methods
spectra<-	imageData-methods
spectra<-,MSImageSet-method	MSImageSet-class
spectrumRepresentation	MSImageProcess-class
spectrumRepresentation,MSImageProcess-method	MSImageProcess-class
spectrumRepresentation<-	MSImageProcess-class
spectrumRepresentation<-,MSImageProcess-method	MSImageProcess-class
stainingMethod	MIAPE-Imaging-class
stainingMethod,MIAPE-Imaging-method	MIAPE-Imaging-class
stainingMethod<-	MIAPE-Imaging-class
stainingMethod<-,MIAPE-Imaging-method	MIAPE-Imaging-class
standardizeSamples	standardizeSamples-methods
standardizeSamples,MSImageSet-method	standardizeSamples-methods
standardizeSamples-methods	standardizeSamples-methods
standardizeSamples.sum	standardizeSamples-methods
storageMode,ImageData-method	ImageData-class
storageMode,iSet-method	iSet-class
storageMode<-,ImageData,character-method	ImageData-class
storageMode<-,iSet,ANY-method	iSet-class
storageMode<-,iSet,character-method	iSet-class
summary,CrossValidated-method	cvApply-methods
summary,iSet-method	iSet-class
summary,OPLS-method	OPLS-methods
summary,PCA-method	PCA-methods
summary,PLS-method	PLS-methods
summary,SpatialKMeans-method	spatialKMeans-methods
summary,SpatialShrunkenCentroids-method	spatialShrunkenCentroids-methods
tissueThickness	MIAPE-Imaging-class
tissueThickness,MIAPE-Imaging-method	MIAPE-Imaging-class
tissueThickness<-	MIAPE-Imaging-class
tissueThickness<-,MIAPE-Imaging-method	MIAPE-Imaging-class
tissueWash	MIAPE-Imaging-class
tissueWash,MIAPE-Imaging-method	MIAPE-Imaging-class
tissueWash<-	MIAPE-Imaging-class
tissueWash<-,MIAPE-Imaging-method	MIAPE-Imaging-class
topLabels	topLabels-methods
topLabels,CrossValidated-method	topLabels-methods
topLabels,OPLS-method	topLabels-methods
topLabels,PCA-method	topLabels-methods
topLabels,PLS-method	topLabels-methods
topLabels,ResultSet-method	topLabels-methods
topLabels,SpatialKMeans-method	topLabels-methods
topLabels,SpatialShrunkenCentroids-method	topLabels-methods
topLabels-methods	topLabels-methods
varLabels,iSet-method	iSet-class
varLabels<-,iSet-method	iSet-class
varMetadata,iSet-method	iSet-class
varMetadata<-,iSet,ANY-method	iSet-class
varMetadata<-,iSet-method	iSet-class
writeAnalyze	writeMSIData
writeAnalyze,MSImageSet-method	writeMSIData
writeImzML	writeMSIData
writeImzML,MSImageSet-method	writeMSIData
writeMSIData	writeMSIData
writeMSIData,MSImageSet,character-method	writeMSIData
[,Binmat,ANY,ANY,ANY-method	Binmat-class
[,Binmat,ANY,ANY,NULL-method	Binmat-class
[,Binmat-method	Binmat-class
[,Hashmat,ANY,ANY,ANY-method	Hashmat-class
[,Hashmat,ANY,ANY,NULL-method	Hashmat-class
[,Hashmat-method	Hashmat-class
[,IAnnotatedDataFrame,ANY,ANY,ANY-method	IAnnotatedDataFrame-class
[,ResultSet,ANY,ANY,ANY-method	ResultSet-class
[,ResultSet-method	ResultSet-class
[,SImageData,ANY,ANY,ANY-method	SImageData-class
[,SImageData,ANY,ANY,NULL-method	SImageData-class
[,SImageData-method	SImageData-class
[,SImageSet,ANY,ANY,ANY-method	SImageSet-class
[,SImageSet-method	SImageSet-class
[<-,Hashmat,ANY,ANY,ANY-method	Hashmat-class
[<-,Hashmat-method	Hashmat-class
[[,ImageData,character,missing-method	ImageData-class
[[,ImageData-method	ImageData-class
[[,iSet,ANY,ANY-method	iSet-class
[[,iSet-method	iSet-class
[[,ResultSet,ANY,ANY-method	ResultSet-class
[[,ResultSet-method	ResultSet-class
[[<-,ImageData,character,missing-method	ImageData-class
[[<-,ImageData-method	ImageData-class
[[<-,iSet,ANY,ANY-method	iSet-class
[[<-,iSet-method	iSet-class
