A mass spectrometry imaging toolbox for statistical analysis

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Documentation for package ‘Cardinal’ version 3.4.3

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

Help Pages

A B C D F G H I J L M N O P R S T V W X misc

Cardinal-package

Mass spectrometry imaging tools

-- A --

addShape	Simulate a mass spectrum or MS imaging experiment
aggregate-method	Calculating summary statistics
alpha.colors	Color palettes for imaging
AnnotatedImage	Deprecated functions and methods in Cardinal
AnnotatedImage-class	Deprecated functions and methods in Cardinal
AnnotatedImageList	Deprecated functions and methods in Cardinal
AnnotatedImageList-class	Deprecated functions and methods in Cardinal
AnnotatedImagingExperiment	Deprecated functions and methods in Cardinal
AnnotatedImagingExperiment-class	Deprecated functions and methods in Cardinal
as.data.frame-method	XDataFrame: DataFrame with eXtra metadata columns
as.env-method	XDataFrame: DataFrame with eXtra metadata columns
as.list-method	ImageList: Abstract image data list
as.list-method	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
as.list-method	MassDataFrame: data frame with mass-to-charge ratio metadata
as.list-method	PositionDataFrame: data frame with spatial position metadata
as.matrix-method	XDataFrame: DataFrame with eXtra metadata columns

-- B --

baselineReduction	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
baselineReduction-method	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
baselineReduction<-	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
baselineReduction<--method	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
batchProcess	Legacy classes and methods in Cardinal
batchProcess-method	Legacy classes and methods in Cardinal
batchProcess-methods	Legacy classes and methods in Cardinal
bw.colors	Color palettes for imaging

-- C --

Cardinal	Mass spectrometry imaging tools
Cardinal-legacy	Legacy classes and methods in Cardinal
Cardinal-reexports	Objects exported from other packages
CardinalLog	Mass spectrometry imaging tools
CardinalVersion	Mass spectrometry imaging tools
cbind-method	ImageList: Abstract image data list
cbind-method	ImagingExperiment: Abstract class for imaging experiments
cbind-method	ImagingResult: Results of statistical analysis of imaging experiments
cbind-method	MSImagingExperiment: Mass spectrometry imaging experiments
cbind-method	MassDataFrame: data frame with mass-to-charge ratio metadata
cbind-method	PositionDataFrame: data frame with spatial position metadata
cbind-method	SparseImagingExperiment: Pixel-sparse imaging experiments
cbind-method	XDataFrame: DataFrame with eXtra metadata columns
cbind-method	Deprecated functions and methods in Cardinal
centroided	MSImagingExperiment: Mass spectrometry imaging experiments
centroided-method	MSImagingExperiment: Mass spectrometry imaging experiments
centroided<-	MSImagingExperiment: Mass spectrometry imaging experiments
centroided<--method	MSImagingExperiment: Mass spectrometry imaging experiments
cividis	Objects exported from other packages
class:AnnotatedImage	Deprecated functions and methods in Cardinal
class:AnnotatedImageList	Deprecated functions and methods in Cardinal
class:AnnotatedImagingExperiment	Deprecated functions and methods in Cardinal
class:Hashmat	Legacy classes and methods in Cardinal
class:IAnnotatedDataFrame	Legacy classes and methods in Cardinal
class:ImageArrayList	ImageList: Abstract image data list
class:ImageData	Legacy classes and methods in Cardinal
class:ImageList	ImageList: Abstract image data list
class:ImagingExperiment	ImagingExperiment: Abstract class for imaging experiments
class:ImagingResult	ImagingResult: Results of statistical analysis of imaging experiments
class:iSet	Legacy classes and methods in Cardinal
class:MassDataFrame	MassDataFrame: data frame with mass-to-charge ratio metadata
class:MeansTest	Linear model-based testing for summarized imaging experiments
class:MIAPE-Imaging	Legacy classes and methods in Cardinal
class:MSContinuousImagingExperiment	MSContinuousImagingExperiment: "Continuous" mass spectrometry imaging experiments
class:MSContinuousImagingSpectraList	ImageList: Abstract image data list
class:MSImageData	Legacy classes and methods in Cardinal
class:MSImageProcess	Legacy classes and methods in Cardinal
class:MSImageSet	Legacy classes and methods in Cardinal
class:MSImagingExperiment	MSImagingExperiment: Mass spectrometry imaging experiments
class:MSImagingInfo	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
class:MSProcessedImagingExperiment	MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments
class:MSProcessedImagingSpectraList	ImageList: Abstract image data list
class:OPLS	Partial least squares
class:PCA	Principal components analysis
class:PLS	Partial least squares
class:PositionDataFrame	PositionDataFrame: data frame with spatial position metadata
class:ResultSet	Legacy classes and methods in Cardinal
class:SegmentationTest	Linear model-based testing for summarized imaging experiments
class:SImageData	Legacy classes and methods in Cardinal
class:SImageSet	Legacy classes and methods in Cardinal
class:SimpleImageArrayList	ImageList: Abstract image data list
class:SimpleImageList	ImageList: Abstract image data list
class:SparseImagingExperiment	SparseImagingExperiment: Pixel-sparse imaging experiments
class:SparseImagingResult	ImagingResult: Results of statistical analysis of imaging experiments
class:SpatialDGMM	Spatially-aware Dirichlet Gaussian mixture model
class:spatialFastmap	Spatially-aware FastMap projection
class:SpatialKMeans	Spatially-aware k-means clustering
class:SpatialShrunkenCentroids	Spatially-aware shrunken centroid clustering and classification
class:XDataFrame	XDataFrame: DataFrame with eXtra metadata columns
col.map	Color palettes for imaging
colocalized	Colocalized features
colocalized-method	Colocalized features
color.map	Color palettes for imaging
combine-method	ImagingExperiment: Abstract class for imaging experiments
combine-method	ImagingResult: Results of statistical analysis of imaging experiments
combine-method	SparseImagingExperiment: Pixel-sparse imaging experiments
combine-method	Deprecated functions and methods in Cardinal
coord	PositionDataFrame: data frame with spatial position metadata
coord-method	PositionDataFrame: data frame with spatial position metadata
coord-method	SparseImagingExperiment: Pixel-sparse imaging experiments
coord-method	Deprecated functions and methods in Cardinal
coord-methods	PositionDataFrame: data frame with spatial position metadata
coord<-	PositionDataFrame: data frame with spatial position metadata
coord<--method	PositionDataFrame: data frame with spatial position metadata
coord<--method	SparseImagingExperiment: Pixel-sparse imaging experiments
coord<--method	Deprecated functions and methods in Cardinal
coordinates	PositionDataFrame: data frame with spatial position metadata
coordinates-method	PositionDataFrame: data frame with spatial position metadata
coordinates-method	SparseImagingExperiment: Pixel-sparse imaging experiments
coordinates-method	Deprecated functions and methods in Cardinal
coordinates-methods	PositionDataFrame: data frame with spatial position metadata
coordinates<-	PositionDataFrame: data frame with spatial position metadata
coordinates<--method	PositionDataFrame: data frame with spatial position metadata
coordinates<--method	SparseImagingExperiment: Pixel-sparse imaging experiments
coordinates<--method	Deprecated functions and methods in Cardinal
coordLabels	PositionDataFrame: data frame with spatial position metadata
coordLabels-method	PositionDataFrame: data frame with spatial position metadata
coordLabels-method	SparseImagingExperiment: Pixel-sparse imaging experiments
coordLabels-methods	PositionDataFrame: data frame with spatial position metadata
coordLabels<-	PositionDataFrame: data frame with spatial position metadata
coordLabels<--method	PositionDataFrame: data frame with spatial position metadata
coordLabels<--method	SparseImagingExperiment: Pixel-sparse imaging experiments
coordnames	PositionDataFrame: data frame with spatial position metadata
coordnames-method	PositionDataFrame: data frame with spatial position metadata
coordnames-method	SparseImagingExperiment: Pixel-sparse imaging experiments
coordnames-methods	PositionDataFrame: data frame with spatial position metadata
coordnames<-	PositionDataFrame: data frame with spatial position metadata
coordnames<--method	PositionDataFrame: data frame with spatial position metadata
coordnames<--method	SparseImagingExperiment: Pixel-sparse imaging experiments
crossValidate	Apply cross-validation to imaging analyses
crossValidate-method	Apply cross-validation to imaging analyses
crossValidate-methods	Apply cross-validation to imaging analyses
cvApply	Apply cross-validation to imaging analyses
cvApply-method	Apply cross-validation to imaging analyses
cvApply-methods	Apply cross-validation to imaging analyses

-- D --

darkmode	Color palettes for imaging
Defunct	Defunct functions and methods in Cardinal
Deprecated	Deprecated functions and methods in Cardinal
dim-method	ImageList: Abstract image data list
dim-method	ImagingExperiment: Abstract class for imaging experiments
dim-method	SparseImagingExperiment: Pixel-sparse imaging experiments
dim-method	Deprecated functions and methods in Cardinal
dimnames-method	ImagingExperiment: Abstract class for imaging experiments
dims-method	ImageList: Abstract image data list
dims-method	PositionDataFrame: data frame with spatial position metadata
dims-method	SparseImagingExperiment: Pixel-sparse imaging experiments
dims-method	Deprecated functions and methods in Cardinal
discrete.colors	Color palettes for imaging
divergent.colors	Color palettes for imaging
domain-method	MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments
domain<--method	MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments

-- F --

fData	ImagingExperiment: Abstract class for imaging experiments
fData-method	ImagingExperiment: Abstract class for imaging experiments
fData-methods	ImagingExperiment: Abstract class for imaging experiments
fData<-	ImagingExperiment: Abstract class for imaging experiments
fData<--method	ImagingExperiment: Abstract class for imaging experiments
featureApply	Apply functions over imaging datasets
featureApply-method	Apply functions over imaging datasets
featureApply-methods	Apply functions over imaging datasets
featureData	ImagingExperiment: Abstract class for imaging experiments
featureData-method	ImagingExperiment: Abstract class for imaging experiments
featureData-methods	ImagingExperiment: Abstract class for imaging experiments
featureData<-	ImagingExperiment: Abstract class for imaging experiments
featureData<--method	ImagingExperiment: Abstract class for imaging experiments
featureNames	ImagingExperiment: Abstract class for imaging experiments
featureNames-method	ImagingExperiment: Abstract class for imaging experiments
featureNames-methods	ImagingExperiment: Abstract class for imaging experiments
featureNames<-	ImagingExperiment: Abstract class for imaging experiments
featureNames<--method	ImagingExperiment: Abstract class for imaging experiments
features	SparseImagingExperiment: Pixel-sparse imaging experiments
features-method	MSImagingExperiment: Mass spectrometry imaging experiments
features-method	SparseImagingExperiment: Pixel-sparse imaging experiments
features-methods	SparseImagingExperiment: Pixel-sparse imaging experiments
findNeighbors	Find spatial neighbors and spatial weightst
findNeighbors-method	Find spatial neighbors and spatial weightst
findNeighbors-methods	Find spatial neighbors and spatial weightst
fitted-method	Partial least squares
fitted-method	Spatially-aware shrunken centroid clustering and classification

-- G --

getCardinalBPPARAM	Mass spectrometry imaging tools
getCardinalDelayProc	Mass spectrometry imaging tools
getCardinalNumBlocks	Mass spectrometry imaging tools
getCardinalVerbose	Mass spectrometry imaging tools
gradient.colors	Color palettes for imaging
gridded	PositionDataFrame: data frame with spatial position metadata
gridded-method	PositionDataFrame: data frame with spatial position metadata
gridded-method	SparseImagingExperiment: Pixel-sparse imaging experiments
gridded<-	PositionDataFrame: data frame with spatial position metadata
gridded<--method	PositionDataFrame: data frame with spatial position metadata
gridded<--method	SparseImagingExperiment: Pixel-sparse imaging experiments

-- H --

Hashmat	Legacy classes and methods in Cardinal
Hashmat-class	Legacy classes and methods in Cardinal
height	Deprecated functions and methods in Cardinal
height-method	Deprecated functions and methods in Cardinal
height<-	Deprecated functions and methods in Cardinal
height<--method	Deprecated functions and methods in Cardinal

-- I --

IAnnotatedDataFrame	Legacy classes and methods in Cardinal
IAnnotatedDataFrame-class	Legacy classes and methods in Cardinal
iData	ImagingExperiment: Abstract class for imaging experiments
iData-method	ImagingExperiment: Abstract class for imaging experiments
iData-methods	ImagingExperiment: Abstract class for imaging experiments
iData<-	ImagingExperiment: Abstract class for imaging experiments
iData<--method	ImagingExperiment: Abstract class for imaging experiments
iData<--method	MSContinuousImagingExperiment: "Continuous" mass spectrometry imaging experiments
iData<--method	MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments
image	Plot an image of the pixel data of an imaging dataset
image-method	Plot an image of the pixel data of an imaging dataset
image-methods	Plot an image of the pixel data of an imaging dataset
image3D	Plot an image of the pixel data of an imaging dataset
image3D-method	Plot an image of the pixel data of an imaging dataset
ImageArrayList	ImageList: Abstract image data list
ImageArrayList-class	ImageList: Abstract image data list
ImageData	Legacy classes and methods in Cardinal
imageData	ImagingExperiment: Abstract class for imaging experiments
ImageData-class	Legacy classes and methods in Cardinal
imageData-method	ImagingExperiment: Abstract class for imaging experiments
imageData-methods	ImagingExperiment: Abstract class for imaging experiments
imageData<-	ImagingExperiment: Abstract class for imaging experiments
imageData<--method	ImagingExperiment: Abstract class for imaging experiments
imageData<--method	MSContinuousImagingExperiment: "Continuous" mass spectrometry imaging experiments
imageData<--method	MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments
ImageList	ImageList: Abstract image data list
ImageList-class	ImageList: Abstract image data list
ImagingExperiment	ImagingExperiment: Abstract class for imaging experiments
ImagingExperiment-class	ImagingExperiment: Abstract class for imaging experiments
ImagingResult	ImagingResult: Results of statistical analysis of imaging experiments
ImagingResult-class	ImagingResult: Results of statistical analysis of imaging experiments
inferno	Objects exported from other packages
initialize-method	MassDataFrame: data frame with mass-to-charge ratio metadata
initialize-method	PositionDataFrame: data frame with spatial position metadata
instrumentModel	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
instrumentModel-method	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
instrumentVendor	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
instrumentVendor-method	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
intensity.colors	Color palettes for imaging
intensityData	MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments
intensityData-method	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
intensityData-method	MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments
intensityData-methods	MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments
intensityData<-	MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments
intensityData<--method	MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments
ionizationType	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
ionizationType-method	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
is3D	SparseImagingExperiment: Pixel-sparse imaging experiments
is3D-method	PositionDataFrame: data frame with spatial position metadata
is3D-method	SparseImagingExperiment: Pixel-sparse imaging experiments
isCentroided	MSImagingExperiment: Mass spectrometry imaging experiments
isCentroided-method	MSImagingExperiment: Mass spectrometry imaging experiments
isCentroided-method	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
isCentroided-method	MassDataFrame: data frame with mass-to-charge ratio metadata
iSet	Legacy classes and methods in Cardinal
iSet-class	Legacy classes and methods in Cardinal

-- J --

jet.colors

Color palettes for imaging

-- L --

lapply-method	XDataFrame: DataFrame with eXtra metadata columns
length-method	ImageList: Abstract image data list
length-method	ImagingExperiment: Abstract class for imaging experiments
length-method	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
length-method	XDataFrame: DataFrame with eXtra metadata columns
length-method	Deprecated functions and methods in Cardinal
lightmode	Color palettes for imaging
lineScanDirection	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
lineScanDirection-method	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
logLik-method	Spatially-aware shrunken centroid clustering and classification

-- M --

magma	Objects exported from other packages
makeFactor	Select regions-of-interest of an imaging dataset
massAnalyzerType	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
massAnalyzerType-method	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
MassDataFrame	MassDataFrame: data frame with mass-to-charge ratio metadata
MassDataFrame-class	MassDataFrame: data frame with mass-to-charge ratio metadata
matrixApplication	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
matrixApplication-method	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
meansTest	Linear model-based testing for summarized imaging experiments
MeansTest-class	Linear model-based testing for summarized imaging experiments
meansTest-method	Linear model-based testing for summarized imaging experiments
meansTest-methods	Linear model-based testing for summarized imaging experiments
MIAPE-Imaging	Legacy classes and methods in Cardinal
MIAPE-Imaging-class	Legacy classes and methods in Cardinal
modelData	ImagingResult: Results of statistical analysis of imaging experiments
modelData-method	ImagingResult: Results of statistical analysis of imaging experiments
modelData<-	ImagingResult: Results of statistical analysis of imaging experiments
modelData<--method	ImagingResult: Results of statistical analysis of imaging experiments
MSContinuousImagingExperiment	MSContinuousImagingExperiment: "Continuous" mass spectrometry imaging experiments
MSContinuousImagingExperiment-class	MSContinuousImagingExperiment: "Continuous" mass spectrometry imaging experiments
MSContinuousImagingSpectraList	ImageList: Abstract image data list
MSContinuousImagingSpectraList-class	ImageList: Abstract image data list
msiInfo	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
msiInfo-method	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
MSImageData	Legacy classes and methods in Cardinal
MSImageData-class	Legacy classes and methods in Cardinal
MSImageProcess	Legacy classes and methods in Cardinal
MSImageProcess-class	Legacy classes and methods in Cardinal
MSImageSet	Legacy classes and methods in Cardinal
MSImageSet-class	Legacy classes and methods in Cardinal
MSImagingExperiment	MSImagingExperiment: Mass spectrometry imaging experiments
MSImagingExperiment-class	MSImagingExperiment: Mass spectrometry imaging experiments
MSImagingInfo	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
MSImagingInfo-class	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
MSProcessedImagingExperiment	MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments
MSProcessedImagingExperiment-class	MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments
MSProcessedImagingSpectraList	ImageList: Abstract image data list
MSProcessedImagingSpectraList-class	ImageList: Abstract image data list
mz	Manipulate mass-to-charge-ratio values
mz-method	MSImagingExperiment: Mass spectrometry imaging experiments
mz-method	MassDataFrame: data frame with mass-to-charge ratio metadata
mz-method	Manipulate mass-to-charge-ratio values
mz-methods	Manipulate mass-to-charge-ratio values
mz<-	Manipulate mass-to-charge-ratio values
mz<--method	MSImagingExperiment: Mass spectrometry imaging experiments
mz<--method	MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments
mz<--method	MassDataFrame: data frame with mass-to-charge ratio metadata
mzAlign	Mass align an imaging dataset
mzAlign-method	Mass align an imaging dataset
mzAlign-methods	Mass align an imaging dataset
mzBin	Mass bin an imaging dataset
mzBin-method	Mass bin an imaging dataset
mzBin-methods	Mass bin an imaging dataset
mzData	MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments
mzData-method	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
mzData-method	MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments
mzData-methods	MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments
mzData<-	MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments
mzData<--method	MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments
mzFilter	Filter the features of an imaging dataset by intensity
mzFilter-method	Filter the features of an imaging dataset by intensity
mzFilter-methods	Filter the features of an imaging dataset by intensity

-- N --

names-method	ImageList: Abstract image data list
names-method	ImagingExperiment: Abstract class for imaging experiments
names-method	XDataFrame: DataFrame with eXtra metadata columns
names<--method	ImageList: Abstract image data list
names<--method	ImagingExperiment: Abstract class for imaging experiments
normalization	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
normalization-method	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
normalization<-	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
normalization<--method	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
normalize	Normalize an imaging dataset
normalize-method	Normalize an imaging dataset
normalize-methods	Normalize an imaging dataset
normalize.reference	Normalize an imaging dataset
normalize.rms	Normalize an imaging dataset
normalize.tic	Normalize an imaging dataset

-- O --

OPLS	Partial least squares
OPLS-class	Partial least squares
OPLS-method	Partial least squares
OPLS-methods	Partial least squares

-- P --

PCA	Principal components analysis
PCA-class	Principal components analysis
PCA-method	Principal components analysis
PCA-methods	Principal components analysis
pData	ImagingExperiment: Abstract class for imaging experiments
pData-method	ImagingExperiment: Abstract class for imaging experiments
pData-methods	ImagingExperiment: Abstract class for imaging experiments
pData<-	ImagingExperiment: Abstract class for imaging experiments
pData<--method	ImagingExperiment: Abstract class for imaging experiments
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
peakBin	Peak bin an imaging dataset
peakBin-method	Peak bin an imaging dataset
peakBin-methods	Peak bin an imaging dataset
peakData	MSImagingExperiment: Mass spectrometry imaging experiments
peakData-method	MSImagingExperiment: Mass spectrometry imaging experiments
peakData-methods	MSImagingExperiment: Mass spectrometry imaging experiments
peakData<-	MSImagingExperiment: Mass spectrometry imaging experiments
peakData<--method	MSImagingExperiment: Mass spectrometry imaging experiments
peakFilter	Filter the features of an imaging dataset by intensity
peakFilter-method	Filter the features of an imaging dataset by intensity
peakFilter-methods	Filter the features of an imaging dataset by intensity
peakFilter.freq	Filter the features of an imaging dataset by intensity
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.mad	Peak pick an imaging dataset
peakPick.simple	Peak pick an imaging dataset
peakPicking	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
peakPicking-method	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
peakPicking<-	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
peakPicking<--method	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
peaks	MSImagingExperiment: Mass spectrometry imaging experiments
peaks-method	MSImagingExperiment: Mass spectrometry imaging experiments
peaks-methods	MSImagingExperiment: Mass spectrometry imaging experiments
peaks<-	MSImagingExperiment: Mass spectrometry imaging experiments
peaks<--method	MSImagingExperiment: Mass spectrometry imaging experiments
phenoData	ImagingExperiment: Abstract class for imaging experiments
phenoData-method	ImagingExperiment: Abstract class for imaging experiments
phenoData-methods	ImagingExperiment: Abstract class for imaging experiments
phenoData<-	ImagingExperiment: Abstract class for imaging experiments
phenoData<--method	ImagingExperiment: Abstract class for imaging experiments
pixelApply	Apply functions over imaging datasets
pixelApply-method	Apply functions over imaging datasets
pixelApply-methods	Apply functions over imaging datasets
pixelData	ImagingExperiment: Abstract class for imaging experiments
pixelData-method	ImagingExperiment: Abstract class for imaging experiments
pixelData-method	SparseImagingExperiment: Pixel-sparse imaging experiments
pixelData-methods	ImagingExperiment: Abstract class for imaging experiments
pixelData<-	ImagingExperiment: Abstract class for imaging experiments
pixelData<--method	ImagingExperiment: Abstract class for imaging experiments
pixelData<--method	SparseImagingExperiment: Pixel-sparse imaging experiments
pixelNames	ImagingExperiment: Abstract class for imaging experiments
pixelNames-method	ImagingExperiment: Abstract class for imaging experiments
pixelNames-method	SparseImagingExperiment: Pixel-sparse imaging experiments
pixelNames-methods	ImagingExperiment: Abstract class for imaging experiments
pixelNames<-	ImagingExperiment: Abstract class for imaging experiments
pixelNames<--method	ImagingExperiment: Abstract class for imaging experiments
pixelNames<--method	SparseImagingExperiment: Pixel-sparse imaging experiments
pixels	SparseImagingExperiment: Pixel-sparse imaging experiments
pixels-method	MSImagingExperiment: Mass spectrometry imaging experiments
pixels-method	SparseImagingExperiment: Pixel-sparse imaging experiments
pixels-methods	SparseImagingExperiment: Pixel-sparse imaging experiments
pixelSize	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
pixelSize-method	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
plasma	Objects exported from other packages
plot	Plot a signal from the feature data of an imaging dataset
plot-method	Plot a signal from the feature data of an imaging dataset
plot-methods	Plot a signal from the feature data of an imaging dataset
PLS	Partial least squares
PLS-class	Partial least squares
PLS-method	Partial least squares
PLS-methods	Partial least squares
PositionDataFrame	PositionDataFrame: data frame with spatial position metadata
PositionDataFrame-class	PositionDataFrame: data frame with spatial position metadata
predict-method	Principal components analysis
predict-method	Partial least squares
predict-method	Spatially-aware shrunken centroid clustering and classification
preproc-method	SparseImagingExperiment: Pixel-sparse imaging experiments
presetImageDef	Simulate a mass spectrum or MS imaging experiment
process	Delayed Processing of Imaging Datasets
process-method	Delayed Processing of Imaging Datasets
process-methods	Delayed Processing of Imaging Datasets
processingData-method	SparseImagingExperiment: Pixel-sparse imaging experiments
processingData<--method	SparseImagingExperiment: Pixel-sparse imaging experiments
pull-method	MSImagingExperiment: Mass spectrometry imaging experiments
pull-method	SparseImagingExperiment: Pixel-sparse imaging experiments

-- R --

range-method	Deprecated functions and methods in Cardinal
rbind-method	ImageList: Abstract image data list
rbind-method	ImagingExperiment: Abstract class for imaging experiments
rbind-method	ImagingResult: Results of statistical analysis of imaging experiments
rbind-method	MSImagingExperiment: Mass spectrometry imaging experiments
rbind-method	MassDataFrame: data frame with mass-to-charge ratio metadata
rbind-method	PositionDataFrame: data frame with spatial position metadata
rbind-method	SparseImagingExperiment: Pixel-sparse imaging experiments
rbind-method	XDataFrame: DataFrame with eXtra metadata columns
rbind-method	Deprecated functions and methods in Cardinal
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.locmin	Reduce the baseline for an imaging dataset
reduceBaseline.median	Reduce the baseline for an imaging dataset
resolution	PositionDataFrame: data frame with spatial position metadata
resolution-method	MSImagingExperiment: Mass spectrometry imaging experiments
resolution-method	MassDataFrame: data frame with mass-to-charge ratio metadata
resolution-method	PositionDataFrame: data frame with spatial position metadata
resolution-method	SparseImagingExperiment: Pixel-sparse imaging experiments
resolution-method	Deprecated functions and methods in Cardinal
resolution<-	PositionDataFrame: data frame with spatial position metadata
resolution<--method	MSImagingExperiment: Mass spectrometry imaging experiments
resolution<--method	MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments
resolution<--method	MassDataFrame: data frame with mass-to-charge ratio metadata
resolution<--method	PositionDataFrame: data frame with spatial position metadata
resolution<--method	SparseImagingExperiment: Pixel-sparse imaging experiments
resolution<--method	Deprecated functions and methods in Cardinal
resultData	ImagingResult: Results of statistical analysis of imaging experiments
resultData-method	ImagingResult: Results of statistical analysis of imaging experiments
resultData<-	ImagingResult: Results of statistical analysis of imaging experiments
resultData<--method	ImagingResult: Results of statistical analysis of imaging experiments
resultNames	ImagingResult: Results of statistical analysis of imaging experiments
resultNames-method	ImagingResult: Results of statistical analysis of imaging experiments
resultNames<-	ImagingResult: Results of statistical analysis of imaging experiments
ResultSet	Legacy classes and methods in Cardinal
ResultSet-class	Legacy classes and methods in Cardinal
risk.colors	Color palettes for imaging
run	PositionDataFrame: data frame with spatial position metadata
run-method	PositionDataFrame: data frame with spatial position metadata
run-method	SparseImagingExperiment: Pixel-sparse imaging experiments
run<-	PositionDataFrame: data frame with spatial position metadata
run<--method	PositionDataFrame: data frame with spatial position metadata
run<--method	SparseImagingExperiment: Pixel-sparse imaging experiments
runNames	PositionDataFrame: data frame with spatial position metadata
runNames-method	PositionDataFrame: data frame with spatial position metadata
runNames-method	SparseImagingExperiment: Pixel-sparse imaging experiments
runNames<-	PositionDataFrame: data frame with spatial position metadata
runNames<--method	PositionDataFrame: data frame with spatial position metadata
runNames<--method	SparseImagingExperiment: Pixel-sparse imaging experiments

-- S --

sampleNames	ImagingExperiment: Abstract class for imaging experiments
sampleNames-method	ImagingExperiment: Abstract class for imaging experiments
sampleNames-methods	ImagingExperiment: Abstract class for imaging experiments
sampleNames<-	ImagingExperiment: Abstract class for imaging experiments
sampleNames<--method	ImagingExperiment: Abstract class for imaging experiments
sampler-method	MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments
sampler<--method	MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments
scanDirection	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
scanDirection-method	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
scanPattern	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
scanPattern-method	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
scanPolarity	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
scanPolarity-method	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
scans-method	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
scanType	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
scanType-method	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
segmentationTest	Linear model-based testing for summarized imaging experiments
SegmentationTest-class	Linear model-based testing for summarized imaging experiments
segmentationTest-method	Linear model-based testing for summarized imaging experiments
segmentationTest-methods	Linear model-based testing for summarized imaging experiments
selectROI	Select regions-of-interest of an imaging dataset
selectROI-method	Select regions-of-interest of an imaging dataset
selectROI-methods	Select regions-of-interest of an imaging dataset
setCardinalBPPARAM	Mass spectrometry imaging tools
setCardinalDelayProc	Mass spectrometry imaging tools
setCardinalNumBlocks	Mass spectrometry imaging tools
setCardinalVerbose	Mass spectrometry imaging tools
setup.layout	Plot a signal from the feature data of an imaging dataset
show-method	ImageList: Abstract image data list
show-method	ImagingExperiment: Abstract class for imaging experiments
show-method	ImagingResult: Results of statistical analysis of imaging experiments
show-method	MSImagingExperiment: Mass spectrometry imaging experiments
show-method	SparseImagingExperiment: Pixel-sparse imaging experiments
show-method	XDataFrame: DataFrame with eXtra metadata columns
show-method	Deprecated functions and methods in Cardinal
showNames	XDataFrame: DataFrame with eXtra metadata columns
showNames-method	MassDataFrame: data frame with mass-to-charge ratio metadata
showNames-method	PositionDataFrame: data frame with spatial position metadata
showNames-method	XDataFrame: DataFrame with eXtra metadata columns
SImageData	Legacy classes and methods in Cardinal
SImageData-class	Legacy classes and methods in Cardinal
SImageSet	Legacy classes and methods in Cardinal
SImageSet-class	Legacy classes and methods in Cardinal
SimpleImageArrayList-class	ImageList: Abstract image data list
SimpleImageList-class	ImageList: Abstract image data list
simulateImage	Simulate a mass spectrum or MS imaging experiment
simulateSpectrum	Simulate a mass spectrum or MS imaging experiment
slice	Slice an image
slice-method	Slice an image
smooth	Smooth the signals of a imaging dataset
smooth-method	Smooth the signals of a imaging dataset
smooth-methods	Smooth the signals of a imaging dataset
smoothing	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
smoothing-method	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
smoothing<-	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
smoothing<--method	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
smoothSignal	Smooth the signals of a imaging dataset
smoothSignal-method	Smooth the signals of a imaging dataset
smoothSignal-methods	Smooth the signals of a imaging dataset
smoothSignal.gaussian	Smooth the signals of a imaging dataset
smoothSignal.ma	Smooth the signals of a imaging dataset
smoothSignal.sgolay	Smooth the signals of a imaging dataset
sort-method	XDataFrame: DataFrame with eXtra metadata columns
SparseImagingExperiment	SparseImagingExperiment: Pixel-sparse imaging experiments
SparseImagingExperiment-class	SparseImagingExperiment: Pixel-sparse imaging experiments
SparseImagingResult	ImagingResult: Results of statistical analysis of imaging experiments
SparseImagingResult-class	ImagingResult: Results of statistical analysis of imaging experiments
spatialApply	Deprecated functions and methods in Cardinal
spatialApply-method	Deprecated functions and methods in Cardinal
spatialApply-methods	Deprecated functions and methods in Cardinal
spatialDGMM	Spatially-aware Dirichlet Gaussian mixture model
SpatialDGMM-class	Spatially-aware Dirichlet Gaussian mixture model
spatialDGMM-method	Spatially-aware Dirichlet Gaussian mixture model
spatialDGMM-methods	Spatially-aware Dirichlet Gaussian mixture model
spatialFastmap	Spatially-aware FastMap projection
spatialFastmap-class	Spatially-aware FastMap projection
spatialFastmap-method	Spatially-aware FastMap projection
spatialFastmap-methods	Spatially-aware FastMap projection
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
spatialWeights	Find spatial neighbors and spatial weightst
spatialWeights-method	Find spatial neighbors and spatial weightst
spatialWeights-methods	Find spatial neighbors and spatial weightst
spectra	MSImagingExperiment: Mass spectrometry imaging experiments
spectra-method	MSImagingExperiment: Mass spectrometry imaging experiments
spectra-methods	MSImagingExperiment: Mass spectrometry imaging experiments
spectra<-	MSImagingExperiment: Mass spectrometry imaging experiments
spectra<--method	MSImagingExperiment: Mass spectrometry imaging experiments
spectraData	MSImagingExperiment: Mass spectrometry imaging experiments
spectraData-method	MSImagingExperiment: Mass spectrometry imaging experiments
spectraData-methods	MSImagingExperiment: Mass spectrometry imaging experiments
spectraData<-	MSImagingExperiment: Mass spectrometry imaging experiments
spectraData<--method	MSImagingExperiment: Mass spectrometry imaging experiments
spectrumRepresentation	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
spectrumRepresentation-method	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
spectrumRepresentation<-	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
spectrumRepresentation<--method	MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
subset-method	Subsetting
subsetFeatures	Subsetting
subsetPixels	Subsetting
summarizeFeatures	Calculating summary statistics
summarizePixels	Calculating summary statistics
summary-method	Principal components analysis
summary-method	Partial least squares
summary-method	Apply cross-validation to imaging analyses
summary-method	Linear model-based testing for summarized imaging experiments
summary-method	Spatially-aware Dirichlet Gaussian mixture model
summary-method	Spatially-aware FastMap projection
summary-method	Spatially-aware k-means clustering
summary-method	Spatially-aware shrunken centroid clustering and classification

-- T --

tolerance-method	MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments
tolerance<--method	MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments
topFeatures	Top-ranked features from imaging analysis results
topFeatures-method	Top-ranked features from imaging analysis results
topFeatures-methods	Top-ranked features from imaging analysis results

-- V --

viridis

Objects exported from other packages

-- W --

width-method	Deprecated functions and methods in Cardinal
width<--method	Deprecated functions and methods in Cardinal
writeAnalyze	Write mass spectrometry imaging data files
writeAnalyze-method	Write mass spectrometry imaging data files
writeImzML	Write mass spectrometry imaging data files
writeImzML-method	Write mass spectrometry imaging data files
writeMSIData	Write mass spectrometry imaging data files
writeMSIData-method	Write mass spectrometry imaging data files

-- X --

XDataFrame	XDataFrame: DataFrame with eXtra metadata columns
XDataFrame-class	XDataFrame: DataFrame with eXtra metadata columns

-- misc --

$-method	ImagingExperiment: Abstract class for imaging experiments
$-method	ImagingResult: Results of statistical analysis of imaging experiments
$<--method	ImagingExperiment: Abstract class for imaging experiments
$<--method	XDataFrame: DataFrame with eXtra metadata columns
%>%	Objects exported from other packages
[-method	ImageList: Abstract image data list
[-method	ImagingExperiment: Abstract class for imaging experiments
[-method	ImagingResult: Results of statistical analysis of imaging experiments
[-method	MSContinuousImagingExperiment: "Continuous" mass spectrometry imaging experiments
[-method	MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments
[-method	MassDataFrame: data frame with mass-to-charge ratio metadata
[-method	PositionDataFrame: data frame with spatial position metadata
[-method	SparseImagingExperiment: Pixel-sparse imaging experiments
[-method	XDataFrame: DataFrame with eXtra metadata columns
[-method	Deprecated functions and methods in Cardinal
[<--method	ImageList: Abstract image data list
[<--method	ImagingExperiment: Abstract class for imaging experiments
[<--method	SparseImagingExperiment: Pixel-sparse imaging experiments
[[-method	ImageList: Abstract image data list
[[-method	ImagingExperiment: Abstract class for imaging experiments
[[-method	ImagingResult: Results of statistical analysis of imaging experiments
[[<--method	ImageList: Abstract image data list
[[<--method	ImagingExperiment: Abstract class for imaging experiments
[[<--method	ImagingResult: Results of statistical analysis of imaging experiments
[[<--method	MSContinuousImagingExperiment: "Continuous" mass spectrometry imaging experiments
[[<--method	MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments
[[<--method	XDataFrame: DataFrame with eXtra metadata columns