# A mass spectrometry imaging toolbox for statistical analysis

## Documentation for package ‘Cardinal’ version 3.2.1

- 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-method | PositionDataFrame: data frame with spatial position metadata
gridded-method | SparseImagingExperiment: Pixel-sparse imaging experiments
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