A mass spectrometry imaging toolbox for statistical analysis


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Documentation for package ‘Cardinal’ version 3.2.1

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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