# A mass spectrometry imaging toolbox for statistical analysis

## Documentation for package ‘Cardinal’ version 3.8.0

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

## Help Pages

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

Cardinal-package | Mass spectrometry imaging tools

## -- A --

addProcessing-method | Apply queued processing to spectra
addShape | Simulate a mass spectrum or MS imaging experiment
aggregate-method | Deprecated and defunct objects in Cardinal
alpha.colors | Deprecated and defunct objects in Cardinal
as_facets | Re-exported objects from Cardinal
as_layers | Re-exported objects from Cardinal

## -- B --

baselineReduction | Deprecated and defunct objects in Cardinal
baselineReduction<- | Deprecated and defunct objects in Cardinal
bin | Bin spectra
bin-method | Bin spectra
bw.colors | Deprecated and defunct objects in Cardinal

## -- C --

c-method | MSImagingArrays: MS imaging data with arbitrary m/z values
c-method | SpectraArrays: List of spectra arrays
c-method | SpectralImagingArrays: Spectral imaging data with arbitrary domain
Cardinal | Mass spectrometry imaging tools
cbind-method | MSImagingExperiment: MS imaging data with shared m/z values
cbind-method | SpectraArrays: List of spectra arrays
cbind-method | SpectralImagingArrays: Spectral imaging data with arbitrary domain
cbind-method | SpectralImagingExperiment: Spectral imaging data with shared domain
cbind-method | XDataFrame: Extended data frame with key columns
centroided-method | MSImagingExperiment: MS imaging data with shared m/z values
centroided<--method | MSImagingExperiment: MS imaging data with shared m/z values
class:Hashmat | Deprecated and defunct objects in Cardinal
class:IAnnotatedDataFrame | Deprecated and defunct objects in Cardinal
class:ImageData | Deprecated and defunct objects in Cardinal
class:iSet | Deprecated and defunct objects in Cardinal
class:MassDataFrame | MassDataFrame: Extended data frame with key columns
class:MeansTest | Linear model-based testing for summarized imaging experiments
class:MIAPE-Imaging | Deprecated and defunct objects in Cardinal
class:MSImageData | Deprecated and defunct objects in Cardinal
class:MSImageProcess | Deprecated and defunct objects in Cardinal
class:MSImageSet | Deprecated and defunct objects in Cardinal
class:MSImagingArrays | MSImagingArrays: MS imaging data with arbitrary m/z values
class:MSImagingExperiment | MSImagingExperiment: MS imaging data with shared m/z values
class:PositionDataFrame | PositionDataFrame: Extended data frame with key columns
class:ResultSet | Deprecated and defunct objects in Cardinal
class:ResultsList | ResultsList: List of modeling results
class:SImageData | Deprecated and defunct objects in Cardinal
class:SImageSet | Deprecated and defunct objects in Cardinal
class:SpatialCV | Cross-validation for spectral imaging data
class:SpatialDGMM | Spatially-aware Dirichlet Gaussian mixture model
class:SpatialFastmap | Spatially-aware FastMap projection
class:SpatialKMeans | Spatially-aware K-means clustering
class:SpatialNMF | Non-negative matrix factorization
class:SpatialOPLS | Partial least squares (projection to latent structures)
class:SpatialPCA | Principal components analysis
class:SpatialPLS | Partial least squares (projection to latent structures)
class:SpatialResults | SpatialResults: Modeling results with spatial metadata
class:SpatialShrunkenCentroids | Spatially-aware shrunken centroid clustering and classification
class:SpectraArrays | SpectraArrays: List of spectra arrays
class:SpectralImagingArrays | SpectralImagingArrays: Spectral imaging data with arbitrary domain
class:SpectralImagingData | SpectralImagingData: Abstract class for spectral imaging data
class:SpectralImagingExperiment | SpectralImagingExperiment: Spectral imaging data with shared domain
class:XDataFrame | XDataFrame: Extended data frame with key columns
class:XDFrame | XDataFrame: Extended data frame with key columns
classNameForDisplay-method | XDataFrame: Extended data frame with key columns
coef-method | Partial least squares (projection to latent structures)
coerce-method | MSImagingExperiment: MS imaging data with shared m/z values
coerce-method | MassDataFrame: Extended data frame with key columns
coerce-method | PositionDataFrame: Extended data frame with key columns
coerce-method | SpectraArrays: List of spectra arrays
coerce-method | XDataFrame: Extended data frame with key columns
coerce-method | Read mass spectrometry imaging data files
col.map | Deprecated and defunct objects in Cardinal
colMeans-method | Summarize a spectral imaging dataset
colnames-method | SpectralImagingExperiment: Spectral imaging data with shared domain
colnames<--method | SpectralImagingExperiment: Spectral imaging data with shared domain
colocalized | Colocalized features
colocalized-method | Colocalized features
color.map | Deprecated and defunct objects in Cardinal
colStats-method | Summarize a spectral imaging dataset
colSums-method | Summarize a spectral imaging dataset
combine-method | SpectraArrays: List of spectra arrays
combine-method | SpectralImagingArrays: Spectral imaging data with arbitrary domain
combine-method | SpectralImagingExperiment: Spectral imaging data with shared domain
convertMSImagingArrays2Experiment | Read mass spectrometry imaging data files
convertMSImagingExperiment2Arrays | Read mass spectrometry imaging data files
coord | PositionDataFrame: Extended data frame with key columns
coord-method | PositionDataFrame: Extended data frame with key columns
coord-method | SpatialResults: Modeling results with spatial metadata
coord-method | SpectralImagingData: Abstract class for spectral imaging data
coord<- | PositionDataFrame: Extended data frame with key columns
coord<--method | PositionDataFrame: Extended data frame with key columns
coord<--method | SpatialResults: Modeling results with spatial metadata
coord<--method | SpectralImagingData: Abstract class for spectral imaging data
coordNames | PositionDataFrame: Extended data frame with key columns
coordNames-method | PositionDataFrame: Extended data frame with key columns
coordNames-method | SpatialResults: Modeling results with spatial metadata
coordNames-method | SpectralImagingData: Abstract class for spectral imaging data
coordNames<- | PositionDataFrame: Extended data frame with key columns
coordNames<--method | PositionDataFrame: Extended data frame with key columns
coordNames<--method | SpatialResults: Modeling results with spatial metadata
coordNames<--method | SpectralImagingData: Abstract class for spectral imaging data
coregister | Colocalized features
cpal | Re-exported objects from Cardinal
cpals | Re-exported objects from Cardinal
crossValidate | Cross-validation for spectral imaging data
cvApply | Deprecated and defunct objects in Cardinal

## -- D --

darkmode | Deprecated and defunct objects in Cardinal
deprecated | Deprecated and defunct objects in Cardinal
dim-method | SpectraArrays: List of spectra arrays
dim-method | SpectralImagingArrays: Spectral imaging data with arbitrary domain
dim-method | SpectralImagingExperiment: Spectral imaging data with shared domain
discrete.colors | Deprecated and defunct objects in Cardinal
divergent.colors | Deprecated and defunct objects in Cardinal
dpal | Re-exported objects from Cardinal
dpals | Re-exported objects from Cardinal
dropkeys | XDataFrame: Extended data frame with key columns
dropkeys-method | XDataFrame: Extended data frame with key columns

## -- E --

estimateDomain | Estimate shared domain
estimateReferenceMz | Estimate shared domain
estimateReferencePeaks | Estimate shared domain
experimentData-method | MSImagingExperiment: MS imaging data with shared m/z values
experimentData<--method | MSImagingExperiment: MS imaging data with shared m/z values

## -- F --

fData-method | SpatialResults: Modeling results with spatial metadata
fData-method | SpectralImagingExperiment: Spectral imaging data with shared domain
fData<--method | SpatialResults: Modeling results with spatial metadata
fData<--method | SpectralImagingExperiment: Spectral imaging data with shared domain
featureApply | Deprecated and defunct objects in Cardinal
featureApply-method | Deprecated and defunct objects in Cardinal
featureData-method | SpatialResults: Modeling results with spatial metadata
featureData-method | SpectralImagingExperiment: Spectral imaging data with shared domain
featureData<--method | SpatialResults: Modeling results with spatial metadata
featureData<--method | SpectralImagingExperiment: Spectral imaging data with shared domain
featureNames-method | SpatialResults: Modeling results with spatial metadata
featureNames-method | SpectralImagingExperiment: Spectral imaging data with shared domain
featureNames<--method | SpatialResults: Modeling results with spatial metadata
featureNames<--method | SpectralImagingExperiment: Spectral imaging data with shared domain
features | Find feature indices
features-method | Find feature indices
fetch-method | SpectraArrays: List of spectra arrays
fetch-method | SpectralImagingData: Abstract class for spectral imaging data
findNeighbors | Find spatial neighbors
findNeighbors-method | Find spatial neighbors
fitted-method | ResultsList: List of modeling results
fitted-method | Cross-validation for spectral imaging data
fitted-method | Partial least squares (projection to latent structures)
fitted-method | SpatialResults: Modeling results with spatial metadata
fitted-method | Spatially-aware shrunken centroid clustering and classification
flash-method | SpectraArrays: List of spectra arrays
flash-method | SpectralImagingData: Abstract class for spectral imaging data

## -- G --

getCardinalBPPARAM | Mass spectrometry imaging tools
getCardinalChunksize | Mass spectrometry imaging tools
getCardinalLogger | Mass spectrometry imaging tools
getCardinalNChunks | Mass spectrometry imaging tools
getCardinalNumBlocks | Deprecated and defunct objects in Cardinal
getCardinalParallel | Mass spectrometry imaging tools
getCardinalSerialize | Mass spectrometry imaging tools
getCardinalVerbose | Mass spectrometry imaging tools
gradient.colors | Deprecated and defunct objects in Cardinal
gridded | Deprecated and defunct objects in Cardinal
gridded<- | Deprecated and defunct objects in Cardinal

## -- H --

Hashmat | Deprecated and defunct objects in Cardinal
Hashmat-class | Deprecated and defunct objects in Cardinal
height | Deprecated and defunct objects in Cardinal
height<- | Deprecated and defunct objects in Cardinal

## -- I --

IAnnotatedDataFrame | Deprecated and defunct objects in Cardinal
IAnnotatedDataFrame-class | Deprecated and defunct objects in Cardinal
iData | Deprecated and defunct objects in Cardinal
iData-method | Deprecated and defunct objects in Cardinal
iData<- | Deprecated and defunct objects in Cardinal
iData<--method | Deprecated and defunct objects in Cardinal
image | Plot images from a spectral imaging dataset
image-method | ResultsList: List of modeling results
image-method | Cross-validation for spectral imaging data
image-method | Spatially-aware Dirichlet Gaussian mixture model
image-method | Spatially-aware FastMap projection
image-method | Spatially-aware K-means clustering
image-method | Non-negative matrix factorization
image-method | Principal components analysis
image-method | Partial least squares (projection to latent structures)
image-method | SpatialResults: Modeling results with spatial metadata
image-method | Spatially-aware shrunken centroid clustering and classification
image-method | Plot images from a spectral imaging dataset
image3D | Plot images from a spectral imaging dataset
image3D-method | Plot images from a spectral imaging dataset
ImageData | Deprecated and defunct objects in Cardinal
ImageData-class | Deprecated and defunct objects in Cardinal
instrumentVendor | Deprecated and defunct objects in Cardinal
intensity-method | MSImagingArrays: MS imaging data with arbitrary m/z values
intensity-method | MSImagingExperiment: MS imaging data with shared m/z values
intensity.colors | Deprecated and defunct objects in Cardinal
intensity<--method | MSImagingArrays: MS imaging data with arbitrary m/z values
intensity<--method | MSImagingExperiment: MS imaging data with shared m/z values
intensityData | Deprecated and defunct objects in Cardinal
intensityData<- | Deprecated and defunct objects in Cardinal
ionizationType | Deprecated and defunct objects in Cardinal
is3D | Deprecated and defunct objects in Cardinal
is3D-method | PositionDataFrame: Extended data frame with key columns
is3D-method | SpectralImagingData: Abstract class for spectral imaging data
isCentroided-method | MSImagingExperiment: MS imaging data with shared m/z values
iSet | Deprecated and defunct objects in Cardinal
iSet-class | Deprecated and defunct objects in Cardinal

## -- J --

jet.colors | Deprecated and defunct objects in Cardinal

## -- K --

keys | XDataFrame: Extended data frame with key columns
keys-method | XDataFrame: Extended data frame with key columns
keys<- | XDataFrame: Extended data frame with key columns
keys<--method | XDataFrame: Extended data frame with key columns

## -- L --

length-method | SpatialResults: Modeling results with spatial metadata
length-method | SpectraArrays: List of spectra arrays
length-method | SpectralImagingArrays: Spectral imaging data with arbitrary domain
length-method | SpectralImagingExperiment: Spectral imaging data with shared domain
lightmode | Deprecated and defunct objects in Cardinal
lineScanDirection | Deprecated and defunct objects in Cardinal
logLik-method | Spatially-aware Dirichlet Gaussian mixture model
logLik-method | Spatially-aware shrunken centroid clustering and classification

## -- M --

makeFactor | Select regions-of-interest in an image
massAnalyzerType | Deprecated and defunct objects in Cardinal
MassDataFrame | MassDataFrame: Extended data frame with key columns
MassDataFrame-class | MassDataFrame: Extended data frame with key columns
matrixApplication | Deprecated and defunct objects in Cardinal
MeansTest | Linear model-based testing for summarized imaging experiments
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
MIAPE-Imaging | Deprecated and defunct objects in Cardinal
MIAPE-Imaging-class | Deprecated and defunct objects in Cardinal
modelData | SpatialResults: Modeling results with spatial metadata
modelData-method | SpatialResults: Modeling results with spatial metadata
modelData<- | SpatialResults: Modeling results with spatial metadata
modelData<--method | SpatialResults: Modeling results with spatial metadata
msiInfo | Deprecated and defunct objects in Cardinal
MSImageData | Deprecated and defunct objects in Cardinal
MSImageData-class | Deprecated and defunct objects in Cardinal
MSImageProcess | Deprecated and defunct objects in Cardinal
MSImageProcess-class | Deprecated and defunct objects in Cardinal
MSImageSet | Deprecated and defunct objects in Cardinal
MSImageSet-class | Deprecated and defunct objects in Cardinal
MSImagingArrays | MSImagingArrays: MS imaging data with arbitrary m/z values
MSImagingArrays-class | MSImagingArrays: MS imaging data with arbitrary m/z values
MSImagingExperiment | MSImagingExperiment: MS imaging data with shared m/z values
MSImagingExperiment-class | MSImagingExperiment: MS imaging data with shared m/z values
mz-method | MSImagingArrays: MS imaging data with arbitrary m/z values
mz-method | MSImagingExperiment: MS imaging data with shared m/z values
mz-method | MassDataFrame: Extended data frame with key columns
mz<--method | MSImagingArrays: MS imaging data with arbitrary m/z values
mz<--method | MSImagingExperiment: MS imaging data with shared m/z values
mz<--method | MassDataFrame: Extended data frame with key columns
mzAlign | Deprecated and defunct objects in Cardinal
mzAlign-method | Deprecated and defunct objects in Cardinal
mzBin | Deprecated and defunct objects in Cardinal
mzBin-method | Deprecated and defunct objects in Cardinal
mzData | Deprecated and defunct objects in Cardinal
mzData<- | Deprecated and defunct objects in Cardinal
mzFilter | Deprecated and defunct objects in Cardinal
mzFilter-method | Deprecated and defunct objects in Cardinal

## -- N --

names-method | SpatialResults: Modeling results with spatial metadata
names-method | SpectraArrays: List of spectra arrays
names-method | SpectralImagingArrays: Spectral imaging data with arbitrary domain
names-method | SpectralImagingExperiment: Spectral imaging data with shared domain
names<--method | SpectraArrays: List of spectra arrays
names<--method | SpectralImagingArrays: Spectral imaging data with arbitrary domain
names<--method | SpectralImagingExperiment: Spectral imaging data with shared domain
names<--method | XDataFrame: Extended data frame with key columns
NMF | Non-negative matrix factorization
NMF-method | Non-negative matrix factorization
normalization | Deprecated and defunct objects in Cardinal
normalization<- | Deprecated and defunct objects in Cardinal
normalize | Normalize spectra
normalize-method | Normalize spectra
nrun-method | PositionDataFrame: Extended data frame with key columns
nrun-method | SpatialResults: Modeling results with spatial metadata
nrun-method | SpectralImagingData: Abstract class for spectral imaging data

## -- O --

OPLS | Partial least squares (projection to latent structures)
OPLS-method | Partial least squares (projection to latent structures)

## -- P --

PCA | Principal components analysis
PCA-method | Principal components analysis
pData-method | SpatialResults: Modeling results with spatial metadata
pData-method | SpectralImagingData: Abstract class for spectral imaging data
pData<--method | SpatialResults: Modeling results with spatial metadata
pData<--method | SpectralImagingData: Abstract class for spectral imaging data
peakAlign | Align peaks across spectra
peakAlign-method | Align peaks across spectra
peakBin | Deprecated and defunct objects in Cardinal
peakData | Deprecated and defunct objects in Cardinal
peakData<- | Deprecated and defunct objects in Cardinal
peakFilter | Deprecated and defunct objects in Cardinal
peakFilter-method | Deprecated and defunct objects in Cardinal
peakPick | Peak pick spectra
peakPick-method | Peak pick spectra
peakPicking | Deprecated and defunct objects in Cardinal
peakPicking<- | Deprecated and defunct objects in Cardinal
peakProcess | Process peaks in mass spectra
peakProcess-method | Process peaks in mass spectra
pixelApply | Deprecated and defunct objects in Cardinal
pixelApply-method | Deprecated and defunct objects in Cardinal
pixelData | SpectralImagingData: Abstract class for spectral imaging data
pixelData-method | SpatialResults: Modeling results with spatial metadata
pixelData-method | SpectralImagingData: Abstract class for spectral imaging data
pixelData<- | SpectralImagingData: Abstract class for spectral imaging data
pixelData<--method | SpatialResults: Modeling results with spatial metadata
pixelData<--method | SpectralImagingData: Abstract class for spectral imaging data
pixelNames | SpectralImagingData: Abstract class for spectral imaging data
pixelNames-method | SpatialResults: Modeling results with spatial metadata
pixelNames-method | SpectralImagingData: Abstract class for spectral imaging data
pixelNames<- | SpectralImagingData: Abstract class for spectral imaging data
pixelNames<--method | SpatialResults: Modeling results with spatial metadata
pixelNames<--method | SpectralImagingData: Abstract class for spectral imaging data
pixels | Find pixel indices
pixels-method | Find pixel indices
pixelSize | Deprecated and defunct objects in Cardinal
plot | Plot spectra from a spectral imaging dataset
plot-image | Plot images from a spectral imaging dataset
plot-method | Linear model-based testing for summarized imaging experiments
plot-method | ResultsList: List of modeling results
plot-method | Spatially-aware Dirichlet Gaussian mixture model
plot-method | Spatially-aware FastMap projection
plot-method | Spatially-aware K-means clustering
plot-method | Non-negative matrix factorization
plot-method | Principal components analysis
plot-method | Partial least squares (projection to latent structures)
plot-method | SpatialResults: Modeling results with spatial metadata
plot-method | Spatially-aware shrunken centroid clustering and classification
plot-method | Plot spectra from a spectral imaging dataset
plot-spectra | Plot spectra from a spectral imaging dataset
PLS | Partial least squares (projection to latent structures)
PLS-method | Partial least squares (projection to latent structures)
PositionDataFrame | PositionDataFrame: Extended data frame with key columns
PositionDataFrame-class | PositionDataFrame: Extended data frame with key columns
predict-method | ResultsList: List of modeling results
predict-method | Spatially-aware FastMap projection
predict-method | Non-negative matrix factorization
predict-method | Principal components analysis
predict-method | Partial least squares (projection to latent structures)
predict-method | Spatially-aware shrunken centroid clustering and classification
presetImageDef | Simulate a mass spectrum or MS imaging experiment
process | Apply queued processing to spectra
process-method | Apply queued processing to spectra
processingData-method | SpectralImagingData: Abstract class for spectral imaging data
processingData<--method | SpectralImagingData: Abstract class for spectral imaging data

## -- R --

rbind-method | MSImagingExperiment: MS imaging data with shared m/z values
rbind-method | SpectraArrays: List of spectra arrays
rbind-method | SpectralImagingArrays: Spectral imaging data with arbitrary domain
rbind-method | SpectralImagingExperiment: Spectral imaging data with shared domain
rbind-method | XDataFrame: Extended data frame with key columns
readAnalyze | Read mass spectrometry imaging data files
readImzML | Read mass spectrometry imaging data files
readMSIData | Read mass spectrometry imaging data files
recalibrate | Recalibrate spectra
recalibrate-method | Recalibrate spectra
reduceBaseline | Reduce baselines in spectra
reduceBaseline-method | Reduce baselines in spectra
reexports | Re-exported objects from Cardinal
reset | Apply queued processing to spectra
residuals-method | Partial least squares (projection to latent structures)
resolution | Deprecated and defunct objects in Cardinal
resolution<- | Deprecated and defunct objects in Cardinal
resultData | Deprecated and defunct objects in Cardinal
resultData<- | Deprecated and defunct objects in Cardinal
resultNames | Deprecated and defunct objects in Cardinal
resultNames<- | Deprecated and defunct objects in Cardinal
ResultSet | Deprecated and defunct objects in Cardinal
ResultSet-class | Deprecated and defunct objects in Cardinal
ResultsList | ResultsList: List of modeling results
ResultsList-class | ResultsList: List of modeling results
risk.colors | Deprecated and defunct objects in Cardinal
rowMeans-method | Summarize a spectral imaging dataset
rownames-method | SpectralImagingExperiment: Spectral imaging data with shared domain
rownames<--method | SpectralImagingExperiment: Spectral imaging data with shared domain
rowStats-method | Summarize a spectral imaging dataset
rowSums-method | Summarize a spectral imaging dataset
run | PositionDataFrame: Extended data frame with key columns
run-method | PositionDataFrame: Extended data frame with key columns
run-method | SpatialResults: Modeling results with spatial metadata
run-method | SpectralImagingData: Abstract class for spectral imaging data
run<- | PositionDataFrame: Extended data frame with key columns
run<--method | PositionDataFrame: Extended data frame with key columns
run<--method | SpatialResults: Modeling results with spatial metadata
run<--method | SpectralImagingData: Abstract class for spectral imaging data
runNames | PositionDataFrame: Extended data frame with key columns
runNames-method | PositionDataFrame: Extended data frame with key columns
runNames-method | SpatialResults: Modeling results with spatial metadata
runNames-method | SpectralImagingData: Abstract class for spectral imaging data
runNames<- | PositionDataFrame: Extended data frame with key columns
runNames<--method | PositionDataFrame: Extended data frame with key columns
runNames<--method | SpatialResults: Modeling results with spatial metadata
runNames<--method | SpectralImagingData: Abstract class for spectral imaging data

## -- S --

saveCardinalLog | Mass spectrometry imaging tools
scanDirection | Deprecated and defunct objects in Cardinal
scanPattern | Deprecated and defunct objects in Cardinal
scanPolarity | Deprecated and defunct objects in Cardinal
scanType | Deprecated and defunct objects in Cardinal
segmentationTest | Linear model-based testing for summarized imaging experiments
selectROI | Select regions-of-interest in an image
selectROI-method | Select regions-of-interest in an image
setCardinalBPPARAM | Mass spectrometry imaging tools
setCardinalChunksize | Mass spectrometry imaging tools
setCardinalLogger | Mass spectrometry imaging tools
setCardinalNChunks | Mass spectrometry imaging tools
setCardinalNumBlocks | Deprecated and defunct objects in Cardinal
setCardinalParallel | Mass spectrometry imaging tools
setCardinalSerialize | Mass spectrometry imaging tools
setCardinalVerbose | Mass spectrometry imaging tools
show-method | MSImagingArrays: MS imaging data with arbitrary m/z values
show-method | MSImagingExperiment: MS imaging data with shared m/z values
show-method | ResultsList: List of modeling results
show-method | SpatialResults: Modeling results with spatial metadata
show-method | SpectraArrays: List of spectra arrays
show-method | SpectralImagingArrays: Spectral imaging data with arbitrary domain
show-method | SpectralImagingData: Abstract class for spectral imaging data
show-method | SpectralImagingExperiment: Spectral imaging data with shared domain
show-method | XDataFrame: Extended data frame with key columns
SImageData | Deprecated and defunct objects in Cardinal
SImageData-class | Deprecated and defunct objects in Cardinal
SImageSet | Deprecated and defunct objects in Cardinal
SImageSet-class | Deprecated and defunct objects in Cardinal
simulateImage | Simulate a mass spectrum or MS imaging experiment
simulateSpectra | Simulate a mass spectrum or MS imaging experiment
simulateSpectrum | Deprecated and defunct objects in Cardinal
slice | Deprecated and defunct objects in Cardinal
sliceImage | Slice an image
smooth | Smooth spectra
smooth-method | Smooth spectra
smoothing | Deprecated and defunct objects in Cardinal
smoothing<- | Deprecated and defunct objects in Cardinal
smoothSignal | Deprecated and defunct objects in Cardinal
smoothSignal-method | Deprecated and defunct objects in Cardinal
SnowfastParam | Re-exported objects from Cardinal
spatialApply | Deprecated and defunct objects in Cardinal
spatialApply-method | Deprecated and defunct objects in Cardinal
SpatialCV | Cross-validation for spectral imaging data
SpatialCV-class | Cross-validation for spectral imaging data
SpatialDGMM | Spatially-aware Dirichlet Gaussian mixture model
spatialDGMM | Spatially-aware Dirichlet Gaussian mixture model
SpatialDGMM-class | Spatially-aware Dirichlet Gaussian mixture model
spatialDGMM-method | Spatially-aware Dirichlet Gaussian mixture model
spatialDists | Calculate spatially-smoothed distances
spatialDists-method | Calculate spatially-smoothed distances
SpatialFastmap | Spatially-aware FastMap projection
spatialFastmap | Spatially-aware FastMap projection
SpatialFastmap-class | Spatially-aware FastMap projection
spatialFastmap-method | Spatially-aware FastMap projection
SpatialKMeans | Spatially-aware K-means clustering
spatialKMeans | Spatially-aware K-means clustering
SpatialKMeans-class | Spatially-aware K-means clustering
spatialKMeans-method | Spatially-aware K-means clustering
SpatialNMF | Non-negative matrix factorization
SpatialNMF-class | Non-negative matrix factorization
SpatialOPLS | Partial least squares (projection to latent structures)
SpatialOPLS-class | Partial least squares (projection to latent structures)
SpatialPCA | Principal components analysis
SpatialPCA-class | Principal components analysis
SpatialPLS | Partial least squares (projection to latent structures)
SpatialPLS-class | Partial least squares (projection to latent structures)
SpatialResults | SpatialResults: Modeling results with spatial metadata
SpatialResults-class | SpatialResults: Modeling results with spatial metadata
SpatialShrunkenCentroids | Spatially-aware shrunken centroid clustering and classification
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
spatialWeights | Calculate spatial weights
spatialWeights-method | Calculate spatial weights
spectra-method | SpectralImagingData: Abstract class for spectral imaging data
spectra<--method | SpectralImagingData: Abstract class for spectral imaging data
SpectraArrays | SpectraArrays: List of spectra arrays
SpectraArrays-class | SpectraArrays: List of spectra arrays
spectraData-method | SpectralImagingData: Abstract class for spectral imaging data
spectraData<--method | SpectralImagingData: Abstract class for spectral imaging data
SpectralImagingArrays | SpectralImagingArrays: Spectral imaging data with arbitrary domain
SpectralImagingArrays-class | SpectralImagingArrays: Spectral imaging data with arbitrary domain
SpectralImagingData | SpectralImagingData: Abstract class for spectral imaging data
SpectralImagingData-class | SpectralImagingData: Abstract class for spectral imaging data
SpectralImagingExperiment | SpectralImagingExperiment: Spectral imaging data with shared domain
SpectralImagingExperiment-class | SpectralImagingExperiment: Spectral imaging data with shared domain
spectraNames-method | SpectralImagingData: Abstract class for spectral imaging data
spectraNames<--method | SpectralImagingData: Abstract class for spectral imaging data
spectrapply | Apply functions over spectra
spectrapply-method | Apply functions over spectra
spectraVariables-method | SpectralImagingData: Abstract class for spectral imaging data
spectrumRepresentation | Deprecated and defunct objects in Cardinal
spectrumRepresentation<- | Deprecated and defunct objects in Cardinal
subset-method | Subset a spectral imaging dataset
subsetFeatures | Subset a spectral imaging dataset
subsetPixels | Subset a spectral imaging dataset
summarizeFeatures | Summarize a spectral imaging dataset
summarizePixels | Summarize a spectral imaging dataset

## -- T --

topFeatures | Spatially-aware shrunken centroid clustering and classification
topFeatures-method | Linear model-based testing for summarized imaging experiments
topFeatures-method | ResultsList: List of modeling results
topFeatures-method | Spatially-aware K-means clustering
topFeatures-method | Partial least squares (projection to latent structures)
topFeatures-method | Spatially-aware shrunken centroid clustering and classification

## -- V --

vizi_engine | Mass spectrometry imaging tools
vizi_par | Mass spectrometry imaging tools
vizi_style | Mass spectrometry imaging tools
vm_used-method | SpectraArrays: List of spectra arrays

## -- W --

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

## -- X --

XDataFrame | XDataFrame: Extended data frame with key columns
XDataFrame-class | XDataFrame: Extended data frame with key columns
XDFrame | XDataFrame: Extended data frame with key columns
XDFrame-class | XDataFrame: Extended data frame with key columns

## -- misc --

$-method | SpatialResults: Modeling results with spatial metadata
$-method | SpectraArrays: List of spectra arrays
$-method | SpectralImagingData: Abstract class for spectral imaging data
$<--method | SpectraArrays: List of spectra arrays
$<--method | SpectralImagingData: Abstract class for spectral imaging data
$<--method | XDataFrame: Extended data frame with key columns
[-method | MassDataFrame: Extended data frame with key columns
[-method | PositionDataFrame: Extended data frame with key columns
[-method | SpectraArrays: List of spectra arrays
[-method | SpectralImagingArrays: Spectral imaging data with arbitrary domain
[-method | SpectralImagingExperiment: Spectral imaging data with shared domain
[-method | XDataFrame: Extended data frame with key columns
[<--method | SpectraArrays: List of spectra arrays
[<--method | SpectralImagingArrays: Spectral imaging data with arbitrary domain
[<--method | SpectralImagingExperiment: Spectral imaging data with shared domain
[<--method | XDataFrame: Extended data frame with key columns
[[-method | SpatialResults: Modeling results with spatial metadata
[[-method | SpectraArrays: List of spectra arrays
[[-method | SpectralImagingData: Abstract class for spectral imaging data
[[<--method | SpectraArrays: List of spectra arrays
[[<--method | SpectralImagingData: Abstract class for spectral imaging data
[[<--method | XDataFrame: Extended data frame with key columns