A mass spectrometry imaging toolbox for statistical analysis

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Documentation for package ‘Cardinal’ version 1.7.0

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A B C D E F G H I K L M N O P R S T V misc

Cardinal-package Mass spectrometry imaging tools

-- A --

abstract-method Class for Storing Mass Spectrometry Imaging Experiment Information
alpha.colors Color Palettes for Imaging
annotatedDataFrameFrom-method Class Containing Arrays of Imaging Data

-- B --

baselineReduction Class Containing Mass Spectral Pre-Processing Information
baselineReduction-method Class Containing Mass Spectral Pre-Processing Information
baselineReduction<- Class Containing Mass Spectral Pre-Processing Information
baselineReduction<--method Class Containing Mass Spectral Pre-Processing Information
batchProcess Batch Pre-Processing on an Imaging Dataset
batchProcess-method Batch Pre-Processing on an Imaging Dataset
batchProcess-methods Batch Pre-Processing on an Imaging Dataset
Binmat On-Disk Matrix Class Using On-Demand Disk Reads
Binmat-class On-Disk Matrix Class Using On-Demand Disk Reads

-- C --

Cardinal Mass spectrometry imaging tools
cbind-method On-Disk Matrix Class Using On-Demand Disk Reads
cbind-method Sparse Matrix Class Using Lists as Hash Tables
centroided Class Containing Mass Spectral Pre-Processing Information
centroided-method Class Containing Mass Spectral Pre-Processing Information
centroided-method Class to Contain Mass Spectrometry Imaging Experiment Data
centroided<- Class Containing Mass Spectral Pre-Processing Information
centroided<--method Class Containing Mass Spectral Pre-Processing Information
centroided<--method Class to Contain Mass Spectrometry Imaging Experiment Data
class:Binmat On-Disk Matrix Class Using On-Demand Disk Reads
class:Hashmat Sparse Matrix Class Using Lists as Hash Tables
class:IAnnotatedDataFrame Class Containing Measured Variables and Their Meta-Data Description for Imaging Experiments
class:ImageData Class Containing Arrays of Imaging Data
class:iSet Class to Contain High-Throughput Imaging Experiment Data and Metadata
class:MIAPE-Imaging Class for Storing Mass Spectrometry Imaging Experiment Information
class:MSImageData Class Containing Mass Spectrometry Image Data
class:MSImageProcess Class Containing Mass Spectral Pre-Processing Information
class:MSImageSet Class to Contain Mass Spectrometry Imaging Experiment Data
class:OPLS Orthogonal Partial Least Squares
class:PCA Principal Components Analysis
class:PLS Partial Least Squares
class:ResultSet Class to Contain Analysis Results for Imaging Experiments
class:SImageData Class Containing Sparse Image Data
class:SImageSet Class to Contain Pixel-Sparse Imaging Data
class:SpatialKMeans Spatially-Aware K-Means Clustering
class:SpatialShrunkenCentroids Spatially-Aware Shrunken Centroid Clustering and Classification
colnames-method On-Disk Matrix Class Using On-Demand Disk Reads
colnames-method Sparse Matrix Class Using Lists as Hash Tables
colnames<--method On-Disk Matrix Class Using On-Demand Disk Reads
colnames<--method Sparse Matrix Class Using Lists as Hash Tables
combine-method Sparse Matrix Class Using Lists as Hash Tables
combine-method Class Containing Measured Variables and Their Meta-Data Description for Imaging Experiments
combine-method Class Containing Arrays of Imaging Data
combine-method Class for Storing Mass Spectrometry Imaging Experiment Information
combine-method Class Containing Mass Spectral Pre-Processing Information
combine-method Class to Contain Mass Spectrometry Imaging Experiment Data
combine-method Class Containing Sparse Image Data
combine-method Class to Contain Pixel-Sparse Imaging Data
combine-method Class to Contain High-Throughput Imaging Experiment Data and Metadata
coord Retrieve Pixel Coordinates from iSets
coord-method Class Containing Measured Variables and Their Meta-Data Description for Imaging Experiments
coord-method Class Containing Sparse Image Data
coord-method Class to Contain High-Throughput Imaging Experiment Data and Metadata
coord-methods Retrieve Pixel Coordinates from iSets
coord<- Retrieve Pixel Coordinates from iSets
coord<--method Class Containing Measured Variables and Their Meta-Data Description for Imaging Experiments
coord<--method Class Containing Sparse Image Data
coord<--method Class to Contain Pixel-Sparse Imaging Data
coord<--method Class to Contain High-Throughput Imaging Experiment Data and Metadata
coordinates Retrieve Pixel Coordinates from iSets
coordinates-methods Retrieve Pixel Coordinates from iSets
coordinates<- Retrieve Pixel Coordinates from iSets
coordLabels Retrieve Pixel Coordinates from iSets
coordLabels-method Class Containing Measured Variables and Their Meta-Data Description for Imaging Experiments
coordLabels-method Class to Contain High-Throughput Imaging Experiment Data and Metadata
coordLabels-methods Retrieve Pixel Coordinates from iSets
coordLabels<- Retrieve Pixel Coordinates from iSets
coordLabels<--method Class Containing Measured Variables and Their Meta-Data Description for Imaging Experiments
coordLabels<--method Class to Contain Pixel-Sparse Imaging Data
coordLabels<--method Class to Contain High-Throughput Imaging Experiment Data and Metadata
coregister Coregister Images
coregister-method Coregister Images
coregister-methods Coregister Images
cvApply Apply Cross-Validated Analysis to Imaging Datasets
cvApply-method Apply Cross-Validated Analysis to Imaging Datasets
cvApply-methods Apply Cross-Validated Analysis to Imaging Datasets

-- D --

dim-method On-Disk Matrix Class Using On-Demand Disk Reads
dim-method Sparse Matrix Class Using Lists as Hash Tables
dim-method Class Containing Arrays of Imaging Data
dim-method Class Containing Sparse Image Data
dim-method Class to Contain High-Throughput Imaging Experiment Data and Metadata
dim<--method On-Disk Matrix Class Using On-Demand Disk Reads
dim<--method Sparse Matrix Class Using Lists as Hash Tables
dimnames-method On-Disk Matrix Class Using On-Demand Disk Reads
dimnames-method Sparse Matrix Class Using Lists as Hash Tables
dimnames<--method On-Disk Matrix Class Using On-Demand Disk Reads
dimnames<--method Sparse Matrix Class Using Lists as Hash Tables
dims-method Class Containing Arrays of Imaging Data
dims-method Class Containing Sparse Image Data
dims-method Class to Contain High-Throughput Imaging Experiment Data and Metadata

-- E --

embeddingMethod Class for Storing Mass Spectrometry Imaging Experiment Information
embeddingMethod-method Class for Storing Mass Spectrometry Imaging Experiment Information
embeddingMethod<- Class for Storing Mass Spectrometry Imaging Experiment Information
embeddingMethod<--method Class for Storing Mass Spectrometry Imaging Experiment Information
experimentData-method Class to Contain High-Throughput Imaging Experiment Data and Metadata
experimentData<--method Class to Contain High-Throughput Imaging Experiment Data and Metadata
expinfo-method Class for Storing Mass Spectrometry Imaging Experiment Information

-- F --

fData-method Class to Contain High-Throughput Imaging Experiment Data and Metadata
fData<--method Class to Contain High-Throughput Imaging Experiment Data and Metadata
featureApply Apply Functions over Imaging Datasets
featureApply-method Apply Functions over Imaging Datasets
featureApply-methods Apply Functions over Imaging Datasets
featureData-method Class to Contain High-Throughput Imaging Experiment Data and Metadata
featureData<--method Class to Contain High-Throughput Imaging Experiment Data and Metadata
featureNames-method Class Containing Sparse Image Data
featureNames-method Class to Contain High-Throughput Imaging Experiment Data and Metadata
featureNames<--method Class Containing Sparse Image Data
featureNames<--method Class to Contain Pixel-Sparse Imaging Data
featureNames<--method Class to Contain High-Throughput Imaging Experiment Data and Metadata
features Retrieve Pixel or Feature Indices Based on Metadata
features-method Retrieve Pixel or Feature Indices Based on Metadata
features-methods Retrieve Pixel or Feature Indices Based on Metadata
files Class Containing Mass Spectral Pre-Processing Information
files-method Class Containing Mass Spectral Pre-Processing Information
files<- Class Containing Mass Spectral Pre-Processing Information
files<--method Class Containing Mass Spectral Pre-Processing Information
fvarLabels-method Class to Contain High-Throughput Imaging Experiment Data and Metadata
fvarLabels<--method Class to Contain High-Throughput Imaging Experiment Data and Metadata
fvarMetadata-method Class to Contain High-Throughput Imaging Experiment Data and Metadata
fvarMetadata<--method Class to Contain High-Throughput Imaging Experiment Data and Metadata

-- G --

generateImage Generate a Simulated Image
generateSpectrum Generate a Simulated Spectrum
gradient.colors Color Palettes for Imaging

-- H --

Hashmat Sparse Matrix Class Using Lists as Hash Tables
Hashmat-class Sparse Matrix Class Using Lists as Hash Tables

-- I --

IAnnotatedDataFrame Class Containing Measured Variables and Their Meta-Data Description for Imaging Experiments
IAnnotatedDataFrame-class Class Containing Measured Variables and Their Meta-Data Description for Imaging Experiments
iData Retrieve Image Data from iSets
iData-method Class Containing Sparse Image Data
iData-method Class to Contain Pixel-Sparse Imaging Data
iData-method Class to Contain High-Throughput Imaging Experiment Data and Metadata
iData-methods Retrieve Image Data from iSets
iData<- Retrieve Image Data from iSets
iData<--method Class Containing Sparse Image Data
iData<--method Class to Contain Pixel-Sparse Imaging Data
iData<--method Class to Contain High-Throughput Imaging Experiment Data and Metadata
image Plot the Pixel-Space of an Imaging Dataset
image-method Plot the Pixel-Space of an Imaging Dataset
image-methods Plot the Pixel-Space of an Imaging Dataset
image3D Plot the Pixel-Space of an Imaging Dataset
image3D-method Plot the Pixel-Space of an Imaging Dataset
image3D-methods Plot the Pixel-Space of an Imaging Dataset
ImageData Class Containing Arrays of Imaging Data
imageData Retrieve Image Data from iSets
ImageData-class Class Containing Arrays of Imaging Data
imageData-method Class to Contain High-Throughput Imaging Experiment Data and Metadata
imageData-methods Retrieve Image Data from iSets
imageData<- Retrieve Image Data from iSets
imageData<--method Class to Contain High-Throughput Imaging Experiment Data and Metadata
imageShape Class for Storing Mass Spectrometry Imaging Experiment Information
imageShape-method Class for Storing Mass Spectrometry Imaging Experiment Information
imageShape<- Class for Storing Mass Spectrometry Imaging Experiment Information
imageShape<--method Class for Storing Mass Spectrometry Imaging Experiment Information
initialize-method On-Disk Matrix Class Using On-Demand Disk Reads
initialize-method Sparse Matrix Class Using Lists as Hash Tables
initialize-method Class Containing Measured Variables and Their Meta-Data Description for Imaging Experiments
initialize-method Class Containing Arrays of Imaging Data
initialize-method Class Containing Mass Spectrometry Image Data
initialize-method Class Containing Mass Spectral Pre-Processing Information
initialize-method Class to Contain Mass Spectrometry Imaging Experiment Data
initialize-method Class Containing Sparse Image Data
initialize-method Class to Contain Pixel-Sparse Imaging Data
initialize-method Class to Contain High-Throughput Imaging Experiment Data and Metadata
inSituChemistry Class for Storing Mass Spectrometry Imaging Experiment Information
inSituChemistry-method Class for Storing Mass Spectrometry Imaging Experiment Information
inSituChemistry<- Class for Storing Mass Spectrometry Imaging Experiment Information
inSituChemistry<--method Class for Storing Mass Spectrometry Imaging Experiment Information
instrumentModel Class for Storing Mass Spectrometry Imaging Experiment Information
instrumentModel-method Class for Storing Mass Spectrometry Imaging Experiment Information
instrumentModel<- Class for Storing Mass Spectrometry Imaging Experiment Information
instrumentModel<--method Class for Storing Mass Spectrometry Imaging Experiment Information
instrumentVendor Class for Storing Mass Spectrometry Imaging Experiment Information
instrumentVendor-method Class for Storing Mass Spectrometry Imaging Experiment Information
instrumentVendor<- Class for Storing Mass Spectrometry Imaging Experiment Information
instrumentVendor<--method Class for Storing Mass Spectrometry Imaging Experiment Information
intensity.colors Color Palettes for Imaging
ionizationType Class for Storing Mass Spectrometry Imaging Experiment Information
ionizationType-method Class for Storing Mass Spectrometry Imaging Experiment Information
ionizationType<- Class for Storing Mass Spectrometry Imaging Experiment Information
ionizationType<--method Class for Storing Mass Spectrometry Imaging Experiment Information
iSet Class to Contain High-Throughput Imaging Experiment Data and Metadata
iSet-class Class to Contain High-Throughput Imaging Experiment Data and Metadata

-- K --

keys Sparse Matrix Class Using Lists as Hash Tables
keys-method Sparse Matrix Class Using Lists as Hash Tables
keys<- Sparse Matrix Class Using Lists as Hash Tables
keys<--method Sparse Matrix Class Using Lists as Hash Tables

-- L --

length-method Class to Contain Analysis Results for Imaging Experiments
lineScanDirection Class for Storing Mass Spectrometry Imaging Experiment Information
lineScanDirection-method Class for Storing Mass Spectrometry Imaging Experiment Information
lineScanDirection<- Class for Storing Mass Spectrometry Imaging Experiment Information
lineScanDirection<--method Class for Storing Mass Spectrometry Imaging Experiment Information
logLik-method Spatially-Aware Shrunken Centroid Clustering and Classification

-- M --

massAnalyzerType Class for Storing Mass Spectrometry Imaging Experiment Information
massAnalyzerType-method Class for Storing Mass Spectrometry Imaging Experiment Information
massAnalyzerType<- Class for Storing Mass Spectrometry Imaging Experiment Information
massAnalyzerType<--method Class for Storing Mass Spectrometry Imaging Experiment Information
matrixApplication Class for Storing Mass Spectrometry Imaging Experiment Information
matrixApplication-method Class for Storing Mass Spectrometry Imaging Experiment Information
matrixApplication<- Class for Storing Mass Spectrometry Imaging Experiment Information
matrixApplication<--method Class for Storing Mass Spectrometry Imaging Experiment Information
MIAPE-Imaging Class for Storing Mass Spectrometry Imaging Experiment Information
MIAPE-Imaging-class Class for Storing Mass Spectrometry Imaging Experiment Information
modelData Class to Contain Analysis Results for Imaging Experiments
modelData-method Class to Contain Analysis Results for Imaging Experiments
modelData<- Class to Contain Analysis Results for Imaging Experiments
modelData<--method Class to Contain Analysis Results for Imaging Experiments
msiInfo Class for Storing Mass Spectrometry Imaging Experiment Information
msiInfo-method Class for Storing Mass Spectrometry Imaging Experiment Information
MSImageData Class Containing Mass Spectrometry Image Data
MSImageData-class Class Containing Mass Spectrometry Image Data
MSImageProcess Class Containing Mass Spectral Pre-Processing Information
MSImageProcess-class Class Containing Mass Spectral Pre-Processing Information
MSImageSet Class to Contain Mass Spectrometry Imaging Experiment Data
MSImageSet-class Class to Contain Mass Spectrometry Imaging Experiment Data
mz Retrieve m/z-values from MSImageSets
mz-method Class to Contain Mass Spectrometry Imaging Experiment Data
mz-methods Retrieve m/z-values from MSImageSets
mz<- Retrieve m/z-values from MSImageSets
mz<--method Class to Contain Mass Spectrometry Imaging Experiment Data
mzData Retrieve Image Data from iSets
mzData-method Class Containing Mass Spectrometry Image Data
mzData-method Class Containing Sparse Image Data
mzData-methods Retrieve Image Data from iSets
mzData<- Retrieve Image Data from iSets
mzData<--method Class Containing Mass Spectrometry Image Data
mzData<--method Class Containing Sparse Image Data

-- N --

names-method Class Containing Arrays of Imaging Data
names-method Class to Contain Analysis Results for Imaging Experiments
names<--method Class Containing Arrays of Imaging Data
normalization Class Containing Mass Spectral Pre-Processing Information
normalization-method Class Containing Mass Spectral Pre-Processing Information
normalization<- Class Containing Mass Spectral Pre-Processing Information
normalization<--method Class Containing Mass Spectral Pre-Processing Information
normalize Normalize an Imaging Dataset
normalize-method Normalize an Imaging Dataset
normalize-methods Normalize an Imaging Dataset
normalize.tic Normalize an Imaging Dataset
notes-method Class for Storing Mass Spectrometry Imaging Experiment Information
notes<--method Class for Storing Mass Spectrometry Imaging Experiment Information

-- O --

OPLS Orthogonal Partial Least Squares
OPLS-class Orthogonal Partial Least Squares
OPLS-method Orthogonal Partial Least Squares
OPLS-methods Orthogonal Partial Least Squares
otherInfo-method Class for Storing Mass Spectrometry Imaging Experiment Information

-- P --

PCA Principal Components Analysis
PCA-class Principal Components Analysis
PCA-method Principal Components Analysis
PCA-methods Principal Components Analysis
pData Retrieve Information on Pixels in iSet-derived Classes
pData-method Sparse Matrix Class Using Lists as Hash Tables
pData-method Class to Contain High-Throughput Imaging Experiment Data and Metadata
pData-methods Retrieve Information on Pixels in iSet-derived Classes
pData<- Retrieve Information on Pixels in iSet-derived Classes
pData<--method Sparse Matrix Class Using Lists as Hash Tables
pData<--method Class to Contain High-Throughput Imaging Experiment Data and Metadata
peakAlign Peak Align an Imaging Dataset
peakAlign-method Peak Align an Imaging Dataset
peakAlign-methods Peak Align an Imaging Dataset
peakAlign.diff Peak Align an Imaging Dataset
peakAlign.DP Peak Align an Imaging Dataset
peakData Retrieve Image Data from iSets
peakData-method Class Containing Mass Spectrometry Image Data
peakData-method Class Containing Sparse Image Data
peakData-methods Retrieve Image Data from iSets
peakData<- Retrieve Image Data from iSets
peakData<--method Class Containing Mass Spectrometry Image Data
peakData<--method Class Containing Sparse Image Data
peakFilter Peak Filter an Imaging Dataset
peakFilter-method Peak Filter an Imaging Dataset
peakFilter-methods Peak Filter an Imaging Dataset
peakFilter.freq Peak Filter an Imaging Dataset
peakPick Peak Pick an Imaging Dataset
peakPick-method Peak Pick an Imaging Dataset
peakPick-methods Peak Pick an Imaging Dataset
peakPick.adaptive Peak Pick an Imaging Dataset
peakPick.limpic Peak Pick an Imaging Dataset
peakPick.simple Peak Pick an Imaging Dataset
peakPicking Class Containing Mass Spectral Pre-Processing Information
peakPicking-method Class Containing Mass Spectral Pre-Processing Information
peakPicking<- Class Containing Mass Spectral Pre-Processing Information
peakPicking<--method Class Containing Mass Spectral Pre-Processing Information
peaks Retrieve Image Data from iSets
peaks-method Class to Contain Mass Spectrometry Imaging Experiment Data
peaks-methods Retrieve Image Data from iSets
peaks<- Retrieve Image Data from iSets
peaks<--method Class to Contain Mass Spectrometry Imaging Experiment Data
pixelApply Apply Functions over Imaging Datasets
pixelApply-method Apply Functions over Imaging Datasets
pixelApply-methods Apply Functions over Imaging Datasets
pixelData Retrieve Information on Pixels in iSet-derived Classes
pixelData-method Class to Contain High-Throughput Imaging Experiment Data and Metadata
pixelData-methods Retrieve Information on Pixels in iSet-derived Classes
pixelData<- Retrieve Information on Pixels in iSet-derived Classes
pixelData<--method Class to Contain High-Throughput Imaging Experiment Data and Metadata
pixelNames Retrieve Pixel Names from iSets
pixelNames-method Class Containing Measured Variables and Their Meta-Data Description for Imaging Experiments
pixelNames-method Class Containing Sparse Image Data
pixelNames-method Class to Contain High-Throughput Imaging Experiment Data and Metadata
pixelNames-methods Retrieve Pixel Names from iSets
pixelNames<- Retrieve Pixel Names from iSets
pixelNames<--method Class Containing Measured Variables and Their Meta-Data Description for Imaging Experiments
pixelNames<--method Class Containing Sparse Image Data
pixelNames<--method Class to Contain Pixel-Sparse Imaging Data
pixelNames<--method Class to Contain High-Throughput Imaging Experiment Data and Metadata
pixels Retrieve Pixel or Feature Indices Based on Metadata
pixels-method Retrieve Pixel or Feature Indices Based on Metadata
pixels-methods Retrieve Pixel or Feature Indices Based on Metadata
pixelSize Class for Storing Mass Spectrometry Imaging Experiment Information
pixelSize-method Class for Storing Mass Spectrometry Imaging Experiment Information
pixelSize<- Class for Storing Mass Spectrometry Imaging Experiment Information
pixelSize<--method Class for Storing Mass Spectrometry Imaging Experiment Information
plot Plot the Feature-Space of an Imaging Dataset
plot-method Plot the Feature-Space of an Imaging Dataset
plot-methods Plot the Feature-Space of an Imaging Dataset
plot.summary.CrossValidated Apply Cross-Validated Analysis to Imaging Datasets
plot.summary.OPLS Orthogonal Partial Least Squares
plot.summary.PCA Principal Components Analysis
plot.summary.PLS Partial Least Squares
plot.summary.SpatialKMeans Spatially-Aware K-Means Clustering
plot.summary.SpatialShrunkenCentroids Spatially-Aware Shrunken Centroid Clustering and Classification
PLS Partial Least Squares
PLS-class Partial Least Squares
PLS-method Partial Least Squares
PLS-methods Partial Least Squares
positionArray Class Containing Sparse Image Data
positionArray-method Class Containing Sparse Image Data
positionArray<- Class Containing Sparse Image Data
positionArray<--method Class Containing Sparse Image Data
predict-method Orthogonal Partial Least Squares
predict-method Principal Components Analysis
predict-method Partial Least Squares
predict-method Spatially-Aware Shrunken Centroid Clustering and Classification
print.summary.CrossValidated Apply Cross-Validated Analysis to Imaging Datasets
print.summary.iSet Class to Contain High-Throughput Imaging Experiment Data and Metadata
print.summary.OPLS Orthogonal Partial Least Squares
print.summary.PCA Principal Components Analysis
print.summary.PLS Partial Least Squares
print.summary.SpatialKMeans Spatially-Aware K-Means Clustering
print.summary.SpatialShrunkenCentroids Spatially-Aware Shrunken Centroid Clustering and Classification
processingData Retrieve Pre-Processing Information from MSImageSets
processingData-method Class to Contain Mass Spectrometry Imaging Experiment Data
processingData-methods Retrieve Pre-Processing Information from MSImageSets
processingData<- Retrieve Pre-Processing Information from MSImageSets
processingData<--method Class to Contain Mass Spectrometry Imaging Experiment Data
prochistory Class Containing Mass Spectral Pre-Processing Information
prochistory-method Class Containing Mass Spectral Pre-Processing Information
prochistory<- Class Containing Mass Spectral Pre-Processing Information
prochistory<--method Class Containing Mass Spectral Pre-Processing Information
protocolData-method Class to Contain High-Throughput Imaging Experiment Data and Metadata
protocolData<--method Class to Contain High-Throughput Imaging Experiment Data and Metadata
pubMedIds-method Class for Storing Mass Spectrometry Imaging Experiment Information
pubMedIds<--method Class for Storing Mass Spectrometry Imaging Experiment Information

-- R --

rbind-method On-Disk Matrix Class Using On-Demand Disk Reads
rbind-method Sparse Matrix Class Using Lists as Hash Tables
readAnalyze Read Mass Spectrometry Imaging Data Files
readImzML Read Mass Spectrometry Imaging Data Files
readMSIData Read Mass Spectrometry Imaging Data Files
reduceBaseline Reduce the Baseline for an Imaging Dataset
reduceBaseline-method Reduce the Baseline for an Imaging Dataset
reduceBaseline-methods Reduce the Baseline for an Imaging Dataset
reduceBaseline.median Reduce the Baseline for an Imaging Dataset
reduceDimension Reduce the Dimension of an Imaging Dataset
reduceDimension-method Reduce the Dimension of an Imaging Dataset
reduceDimension-methods Reduce the Dimension of an Imaging Dataset
reduceDimension.bin Reduce the Dimension of an Imaging Dataset
reduceDimension.peaks Reduce the Dimension of an Imaging Dataset
reduceDimension.resample Reduce the Dimension of an Imaging Dataset
regeneratePositions Class Containing Sparse Image Data
regeneratePositions-method Class Containing Sparse Image Data
regeneratePositions-method Class to Contain Pixel-Sparse Imaging Data
resultData Class to Contain Analysis Results for Imaging Experiments
resultData-method Class to Contain Analysis Results for Imaging Experiments
resultData<- Class to Contain Analysis Results for Imaging Experiments
resultData<--method Class to Contain Analysis Results for Imaging Experiments
ResultSet Class to Contain Analysis Results for Imaging Experiments
ResultSet-class Class to Contain Analysis Results for Imaging Experiments
risk.colors Color Palettes for Imaging
rownames-method On-Disk Matrix Class Using On-Demand Disk Reads
rownames-method Sparse Matrix Class Using Lists as Hash Tables
rownames<--method On-Disk Matrix Class Using On-Demand Disk Reads
rownames<--method Sparse Matrix Class Using Lists as Hash Tables

-- S --

sampleNames-method Class Containing Measured Variables and Their Meta-Data Description for Imaging Experiments
sampleNames-method Class to Contain High-Throughput Imaging Experiment Data and Metadata
sampleNames<--method Class Containing Measured Variables and Their Meta-Data Description for Imaging Experiments
sampleNames<--method Class to Contain High-Throughput Imaging Experiment Data and Metadata
samples-method Class for Storing Mass Spectrometry Imaging Experiment Information
scanDirection Class for Storing Mass Spectrometry Imaging Experiment Information
scanDirection-method Class for Storing Mass Spectrometry Imaging Experiment Information
scanDirection<- Class for Storing Mass Spectrometry Imaging Experiment Information
scanDirection<--method Class for Storing Mass Spectrometry Imaging Experiment Information
scanPattern Class for Storing Mass Spectrometry Imaging Experiment Information
scanPattern-method Class for Storing Mass Spectrometry Imaging Experiment Information
scanPattern<- Class for Storing Mass Spectrometry Imaging Experiment Information
scanPattern<--method Class for Storing Mass Spectrometry Imaging Experiment Information
scanPolarity Class for Storing Mass Spectrometry Imaging Experiment Information
scanPolarity-method Class for Storing Mass Spectrometry Imaging Experiment Information
scanPolarity<- Class for Storing Mass Spectrometry Imaging Experiment Information
scanPolarity<--method Class for Storing Mass Spectrometry Imaging Experiment Information
scanType Class for Storing Mass Spectrometry Imaging Experiment Information
scanType-method Class for Storing Mass Spectrometry Imaging Experiment Information
scanType<- Class for Storing Mass Spectrometry Imaging Experiment Information
scanType<--method Class for Storing Mass Spectrometry Imaging Experiment Information
select Select Regions of an Imaging Dataset
select-method Select Regions of an Imaging Dataset
select-methods Select Regions of an Imaging Dataset
show-method On-Disk Matrix Class Using On-Demand Disk Reads
show-method Sparse Matrix Class Using Lists as Hash Tables
show-method Class Containing Arrays of Imaging Data
show-method Class for Storing Mass Spectrometry Imaging Experiment Information
show-method Class Containing Mass Spectral Pre-Processing Information
show-method Class to Contain Analysis Results for Imaging Experiments
SImageData Class Containing Sparse Image Data
SImageData-class Class Containing Sparse Image Data
SImageSet Class to Contain Pixel-Sparse Imaging Data
SImageSet-class Class to Contain Pixel-Sparse Imaging Data
smoothing Class Containing Mass Spectral Pre-Processing Information
smoothing-method Class Containing Mass Spectral Pre-Processing Information
smoothing<- Class Containing Mass Spectral Pre-Processing Information
smoothing<--method Class Containing Mass Spectral Pre-Processing Information
smoothSignal Smooth the Feature-Vectors of an Imaging Dataset
smoothSignal-method Smooth the Feature-Vectors of an Imaging Dataset
smoothSignal-methods Smooth the Feature-Vectors of an Imaging Dataset
smoothSignal.gaussian Smooth the Feature-Vectors of an Imaging Dataset
smoothSignal.ma Smooth the Feature-Vectors of an Imaging Dataset
smoothSignal.sgolay Smooth the Feature-Vectors of an Imaging Dataset
softwareName Class for Storing Mass Spectrometry Imaging Experiment Information
softwareName-method Class for Storing Mass Spectrometry Imaging Experiment Information
softwareName<- Class for Storing Mass Spectrometry Imaging Experiment Information
softwareName<--method Class for Storing Mass Spectrometry Imaging Experiment Information
softwareVersion Class for Storing Mass Spectrometry Imaging Experiment Information
softwareVersion-method Class for Storing Mass Spectrometry Imaging Experiment Information
softwareVersion<- Class for Storing Mass Spectrometry Imaging Experiment Information
softwareVersion<--method Class for Storing Mass Spectrometry Imaging Experiment Information
spatialKMeans Spatially-Aware K-Means Clustering
SpatialKMeans-class Spatially-Aware K-Means Clustering
spatialKMeans-method Spatially-Aware K-Means Clustering
spatialKMeans-methods Spatially-Aware K-Means Clustering
spatialShrunkenCentroids Spatially-Aware Shrunken Centroid Clustering and Classification
SpatialShrunkenCentroids-class Spatially-Aware Shrunken Centroid Clustering and Classification
spatialShrunkenCentroids-method Spatially-Aware Shrunken Centroid Clustering and Classification
spatialShrunkenCentroids-methods Spatially-Aware Shrunken Centroid Clustering and Classification
specimenOrigin Class for Storing Mass Spectrometry Imaging Experiment Information
specimenOrigin-method Class for Storing Mass Spectrometry Imaging Experiment Information
specimenOrigin<- Class for Storing Mass Spectrometry Imaging Experiment Information
specimenOrigin<--method Class for Storing Mass Spectrometry Imaging Experiment Information
specimenType Class for Storing Mass Spectrometry Imaging Experiment Information
specimenType-method Class for Storing Mass Spectrometry Imaging Experiment Information
specimenType<- Class for Storing Mass Spectrometry Imaging Experiment Information
specimenType<--method Class for Storing Mass Spectrometry Imaging Experiment Information
spectra Retrieve Image Data from iSets
spectra-method Class to Contain Mass Spectrometry Imaging Experiment Data
spectra-methods Retrieve Image Data from iSets
spectra<- Retrieve Image Data from iSets
spectra<--method Class to Contain Mass Spectrometry Imaging Experiment Data
spectrumRepresentation Class Containing Mass Spectral Pre-Processing Information
spectrumRepresentation-method Class Containing Mass Spectral Pre-Processing Information
spectrumRepresentation<- Class Containing Mass Spectral Pre-Processing Information
spectrumRepresentation<--method Class Containing Mass Spectral Pre-Processing Information
stainingMethod Class for Storing Mass Spectrometry Imaging Experiment Information
stainingMethod-method Class for Storing Mass Spectrometry Imaging Experiment Information
stainingMethod<- Class for Storing Mass Spectrometry Imaging Experiment Information
stainingMethod<--method Class for Storing Mass Spectrometry Imaging Experiment Information
standardizeSamples Standardize the Samples in an Imaging Dataset
standardizeSamples-method Standardize the Samples in an Imaging Dataset
standardizeSamples-methods Standardize the Samples in an Imaging Dataset
standardizeSamples.sum Standardize the Samples in an Imaging Dataset
storageMode-method Class Containing Arrays of Imaging Data
storageMode-method Class to Contain High-Throughput Imaging Experiment Data and Metadata
storageMode<--method Class Containing Arrays of Imaging Data
storageMode<--method Class to Contain High-Throughput Imaging Experiment Data and Metadata
summary-method Orthogonal Partial Least Squares
summary-method Principal Components Analysis
summary-method Partial Least Squares
summary-method Apply Cross-Validated Analysis to Imaging Datasets
summary-method Class to Contain High-Throughput Imaging Experiment Data and Metadata
summary-method Spatially-Aware K-Means Clustering
summary-method Spatially-Aware Shrunken Centroid Clustering and Classification

-- T --

tissueThickness Class for Storing Mass Spectrometry Imaging Experiment Information
tissueThickness-method Class for Storing Mass Spectrometry Imaging Experiment Information
tissueThickness<- Class for Storing Mass Spectrometry Imaging Experiment Information
tissueThickness<--method Class for Storing Mass Spectrometry Imaging Experiment Information
tissueWash Class for Storing Mass Spectrometry Imaging Experiment Information
tissueWash-method Class for Storing Mass Spectrometry Imaging Experiment Information
tissueWash<- Class for Storing Mass Spectrometry Imaging Experiment Information
tissueWash<--method Class for Storing Mass Spectrometry Imaging Experiment Information
topLabels Retrieve Top-Ranked Labels from Analysis Results
topLabels-method Retrieve Top-Ranked Labels from Analysis Results
topLabels-methods Retrieve Top-Ranked Labels from Analysis Results

-- V --

varLabels-method Class to Contain High-Throughput Imaging Experiment Data and Metadata
varLabels<--method Class to Contain High-Throughput Imaging Experiment Data and Metadata
varMetadata-method Class to Contain High-Throughput Imaging Experiment Data and Metadata
varMetadata<--method Class to Contain High-Throughput Imaging Experiment Data and Metadata

-- misc --

$-method Class to Contain Analysis Results for Imaging Experiments
$-method Class to Contain High-Throughput Imaging Experiment Data and Metadata
$<--method Class to Contain High-Throughput Imaging Experiment Data and Metadata
[-method On-Disk Matrix Class Using On-Demand Disk Reads
[-method Sparse Matrix Class Using Lists as Hash Tables
[-method Class Containing Measured Variables and Their Meta-Data Description for Imaging Experiments
[-method Class to Contain Analysis Results for Imaging Experiments
[-method Class Containing Sparse Image Data
[-method Class to Contain Pixel-Sparse Imaging Data
[<--method Sparse Matrix Class Using Lists as Hash Tables
[[-method Class Containing Arrays of Imaging Data
[[-method Class to Contain Analysis Results for Imaging Experiments
[[-method Class to Contain High-Throughput Imaging Experiment Data and Metadata
[[<--method Class Containing Arrays of Imaging Data
[[<--method Class to Contain High-Throughput Imaging Experiment Data and Metadata