# A mass spectrometry imaging toolbox for statistical analysis

## Documentation for package ‘Cardinal’ version 1.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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