# A mass spectrometry imaging toolbox for statistical analysis

## Documentation for package ‘Cardinal’ version 2.2.6

- 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 U V W X misc

Cardinal-package | Mass spectrometry imaging tools

## -- A --

abstract-method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
addShape | Simulate a mass spectrum or MS imaging experiment
alpha.colors | Color palettes for imaging
annotatedDataFrameFrom-method | ImageData: Class containing arrays of imaging data
arrange-method | Data transformation and summarization
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 | MSImageProcess: Class containing mass spectral preprocessing information
baselineReduction-method | MSImageProcess: Class containing mass spectral preprocessing information
baselineReduction-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
baselineReduction<- | MSImageProcess: Class containing mass spectral preprocessing information
baselineReduction<--method | MSImageProcess: Class containing mass spectral preprocessing information
baselineReduction<--method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
batchProcess | Batch Pre-Processing on an Imaging Dataset
batchProcess-method | Batch Pre-Processing on an Imaging Dataset
batchProcess-methods | Batch Pre-Processing on an Imaging Dataset
Binmat | Deprecated functions and methods in Cardinal
Binmat-class | Deprecated functions and methods in Cardinal
bw.colors | Color palettes for imaging

## -- C --

Cardinal | Mass spectrometry imaging tools
Cardinal-defunct | Defunct functions and methods in Cardinal
Cardinal-deprecated | Deprecated functions and methods in Cardinal
Cardinal-reexports | Objects exported from other packages
cbind-method | Hashmat: Sparse matrix class using lists as hash tables
cbind-method | ImageList: Abstract image data list
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 | ResultImagingExperiment: Results of statistical analysis of imaging experiments
cbind-method | SparseImagingExperiment: Pixel-sparse imaging experiments
cbind-method | XDataFrame: DataFrame with eXtra metadata columns
centroided | MSImageProcess: Class containing mass spectral preprocessing information
centroided-method | MSImageProcess: Class containing mass spectral preprocessing information
centroided-method | MSImageSet: Class to contain mass spectrometry imaging experiment data
centroided-method | MSImagingExperiment: Mass spectrometry imaging experiments
centroided<- | MSImageProcess: Class containing mass spectral preprocessing information
centroided<--method | MSImageProcess: Class containing mass spectral preprocessing information
centroided<--method | MSImageSet: Class to contain mass spectrometry imaging experiment data
centroided<--method | MSImagingExperiment: Mass spectrometry imaging experiments
cividis | Objects exported from other packages
class:Binmat | Deprecated functions and methods in Cardinal
class:Hashmat | Hashmat: Sparse matrix class using lists as hash tables
class:IAnnotatedDataFrame | IAnnotatedDataFrame: Class containing measured variables and their metadata for imaging experiments
class:ImageArrayList | ImageList: Abstract image data list
class:ImageData | ImageData: Class containing arrays of imaging data
class:ImageList | ImageList: Abstract image data list
class:ImagingExperiment | ImagingExperiment: Abstract class for imaging experiments
class:iSet | iSet: Class to contain high-throughput imaging experiment data and metadata
class:MassDataFrame | MassDataFrame: data frame with mass-to-charge ratio metadata
class:MeansTest | Linear model-based testing for summarized imaging experiments
class:MIAPE-Imaging | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
class:MSContinuousImagingExperiment | MSContinuousImagingExperiment: Dense mass spectrometry imaging experiments
class:MSContinuousImagingSpectraList | ImageList: Abstract image data list
class:MSImageData | MSImageData: Class containing mass spectrometry image data
class:MSImageProcess | MSImageProcess: Class containing mass spectral preprocessing information
class:MSImageSet | MSImageSet: Class to contain mass spectrometry imaging experiment data
class:MSImagingExperiment | MSImagingExperiment: Mass spectrometry imaging experiments
class:MSImagingInfo | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
class:MSProcessedImagingExperiment | MSProcessedImagingExperiment: Dense 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:ResultImagingExperiment | ResultImagingExperiment: Results of statistical analysis of imaging experiments
class:ResultSet | ResultSet: Class to contain analysis results for imaging experiments
class:SegmentationTest | Linear model-based testing for summarized imaging experiments
class:SImageData | SImageData: Class containing sparse image data
class:SImageSet | SIMageSet: Class to contain pixel-sparse imaging data
class:SimpleImageArrayList | ImageList: Abstract image data list
class:SimpleImageList | ImageList: Abstract image data list
class:SparseImagingExperiment | SparseImagingExperiment: Pixel-sparse imaging experiments
class:SparseResultImagingExperiment | ResultImagingExperiment: 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:SummaryDataFrame | SummaryDataFrame: DataFrame for object summaries
class:XDataFrame | XDataFrame: DataFrame with eXtra metadata columns
col.map | Color palettes for imaging
collect-method | MSImagingExperiment: Mass spectrometry imaging experiments
collect-method | MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
collect-method | SparseImagingExperiment: Pixel-sparse imaging experiments
colnames-method | Hashmat: Sparse matrix class using lists as hash tables
colnames<--method | Hashmat: Sparse matrix class using lists as hash tables
colocalized | Colocalized features
colocalized-method | Colocalized features
color.map | Color palettes for imaging
combine-method | Hashmat: Sparse matrix class using lists as hash tables
combine-method | IAnnotatedDataFrame: Class containing measured variables and their metadata for imaging experiments
combine-method | ImageData: Class containing arrays of imaging data
combine-method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
combine-method | MSImageProcess: Class containing mass spectral preprocessing information
combine-method | MSImageSet: Class to contain mass spectrometry imaging experiment data
combine-method | ResultImagingExperiment: Results of statistical analysis of imaging experiments
combine-method | SImageData: Class containing sparse image data
combine-method | SIMageSet: Class to contain pixel-sparse imaging data
combine-method | SparseImagingExperiment: Pixel-sparse imaging experiments
combine-method | iSet: Class to contain high-throughput imaging experiment data and metadata
combiner-method | MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
combiner<--method | MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
coord | PositionDataFrame: data frame with spatial position metadata
coord-method | IAnnotatedDataFrame: Class containing measured variables and their metadata for imaging experiments
coord-method | PositionDataFrame: data frame with spatial position metadata
coord-method | SImageData: Class containing sparse image data
coord-method | SparseImagingExperiment: Pixel-sparse imaging experiments
coord-method | iSet: Class to contain high-throughput imaging experiment data and metadata
coord-methods | PositionDataFrame: data frame with spatial position metadata
coord<- | PositionDataFrame: data frame with spatial position metadata
coord<--method | IAnnotatedDataFrame: Class containing measured variables and their metadata for imaging experiments
coord<--method | PositionDataFrame: data frame with spatial position metadata
coord<--method | SImageData: Class containing sparse image data
coord<--method | SIMageSet: Class to contain pixel-sparse imaging data
coord<--method | SparseImagingExperiment: Pixel-sparse imaging experiments
coord<--method | iSet: Class to contain high-throughput imaging experiment data and 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-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
coordLabels | PositionDataFrame: data frame with spatial position metadata
coordLabels-method | IAnnotatedDataFrame: Class containing measured variables and their metadata for imaging experiments
coordLabels-method | PositionDataFrame: data frame with spatial position metadata
coordLabels-method | SparseImagingExperiment: Pixel-sparse imaging experiments
coordLabels-method | iSet: Class to contain high-throughput imaging experiment data and metadata
coordLabels-methods | PositionDataFrame: data frame with spatial position metadata
coordLabels<- | PositionDataFrame: data frame with spatial position metadata
coordLabels<--method | IAnnotatedDataFrame: Class containing measured variables and their metadata for imaging experiments
coordLabels<--method | PositionDataFrame: data frame with spatial position metadata
coordLabels<--method | SIMageSet: Class to contain pixel-sparse imaging data
coordLabels<--method | SparseImagingExperiment: Pixel-sparse imaging experiments
coordLabels<--method | iSet: Class to contain high-throughput imaging experiment data and 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
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
coregister | Coregister images
coregister-method | Coregister images
coregister-methods | Coregister images
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
dim-method | Hashmat: Sparse matrix class using lists as hash tables
dim-method | ImageData: Class containing arrays of imaging data
dim-method | ImageList: Abstract image data list
dim-method | ImagingExperiment: Abstract class for imaging experiments
dim-method | SImageData: Class containing sparse image data
dim-method | iSet: Class to contain high-throughput imaging experiment data and metadata
dim<--method | Hashmat: Sparse matrix class using lists as hash tables
dimnames-method | Hashmat: Sparse matrix class using lists as hash tables
dimnames-method | ImagingExperiment: Abstract class for imaging experiments
dimnames<--method | Hashmat: Sparse matrix class using lists as hash tables
dims-method | ImageData: Class containing arrays of imaging data
dims-method | ImageList: Abstract image data list
dims-method | PositionDataFrame: data frame with spatial position metadata
dims-method | SImageData: Class containing sparse image data
dims-method | SparseImagingExperiment: Pixel-sparse imaging experiments
dims-method | iSet: Class to contain high-throughput imaging experiment data and metadata
discrete.colors | Color palettes for imaging
divergent.colors | Color palettes for imaging

## -- E --

embeddingMethod | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
embeddingMethod-method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
embeddingMethod<- | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
embeddingMethod<--method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
experimentData-method | iSet: Class to contain high-throughput imaging experiment data and metadata
experimentData<--method | iSet: Class to contain high-throughput imaging experiment data and metadata
expinfo-method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information

## -- F --

fData | ImagingExperiment: Abstract class for imaging experiments
fData-method | ImagingExperiment: Abstract class for imaging experiments
fData-method | iSet: Class to contain high-throughput imaging experiment data and metadata
fData-methods | ImagingExperiment: Abstract class for imaging experiments
fData<- | ImagingExperiment: Abstract class for imaging experiments
fData<--method | ImagingExperiment: Abstract class for imaging experiments
fData<--method | iSet: Class to contain high-throughput imaging experiment data and metadata
featureApply | Apply functions over imaging datasets
featureApply-method | Apply functions over imaging datasets
featureApply-methods | Apply functions over imaging datasets
featureData | ImagingExperiment: Abstract class for imaging experiments
featureData-method | ImagingExperiment: Abstract class for imaging experiments
featureData-method | iSet: Class to contain high-throughput imaging experiment data and metadata
featureData-methods | ImagingExperiment: Abstract class for imaging experiments
featureData<- | ImagingExperiment: Abstract class for imaging experiments
featureData<--method | ImagingExperiment: Abstract class for imaging experiments
featureData<--method | iSet: Class to contain high-throughput imaging experiment data and metadata
featureNames | ImagingExperiment: Abstract class for imaging experiments
featureNames-method | ImagingExperiment: Abstract class for imaging experiments
featureNames-method | SImageData: Class containing sparse image data
featureNames-method | iSet: Class to contain high-throughput imaging experiment data and metadata
featureNames-methods | ImagingExperiment: Abstract class for imaging experiments
featureNames<- | ImagingExperiment: Abstract class for imaging experiments
featureNames<--method | ImagingExperiment: Abstract class for imaging experiments
featureNames<--method | SImageData: Class containing sparse image data
featureNames<--method | SIMageSet: Class to contain pixel-sparse imaging data
featureNames<--method | iSet: Class to contain high-throughput imaging experiment data and metadata
features | ImagingExperiment: Abstract class for imaging experiments
features-method | ImagingExperiment: Abstract class for imaging experiments
features-method | MSImageSet: Class to contain mass spectrometry imaging experiment data
features-method | MSImagingExperiment: Mass spectrometry imaging experiments
features-method | iSet: Class to contain high-throughput imaging experiment data and metadata
features-methods | ImagingExperiment: Abstract class for imaging experiments
files | MSImageProcess: Class containing mass spectral preprocessing information
files-method | MSImageProcess: Class containing mass spectral preprocessing information
files<- | MSImageProcess: Class containing mass spectral preprocessing information
files<--method | MSImageProcess: Class containing mass spectral preprocessing information
filter | Data transformation and summarization
filter-method | Data transformation and summarization
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
fvarLabels-method | iSet: Class to contain high-throughput imaging experiment data and metadata
fvarLabels<--method | iSet: Class to contain high-throughput imaging experiment data and metadata
fvarMetadata-method | iSet: Class to contain high-throughput imaging experiment data and metadata
fvarMetadata<--method | iSet: Class to contain high-throughput imaging experiment data and metadata

## -- G --

generateImage | Generate a simulated spectrum or image
generateSpectrum | Generate a simulated spectrum or image
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
groups | Objects exported from other packages
groups-method | XDataFrame: DataFrame with eXtra metadata columns
group_by | Objects exported from other packages
group_by-method | Data transformation and summarization

## -- H --

Hashmat | Hashmat: Sparse matrix class using lists as hash tables
Hashmat-class | Hashmat: Sparse matrix class using lists as hash tables

## -- I --

IAnnotatedDataFrame | IAnnotatedDataFrame: Class containing measured variables and their metadata for imaging experiments
IAnnotatedDataFrame-class | IAnnotatedDataFrame: Class containing measured variables and their metadata for imaging experiments
iData | ImagingExperiment: Abstract class for imaging experiments
iData-method | ImagingExperiment: Abstract class for imaging experiments
iData-method | SImageData: Class containing sparse image data
iData-method | SIMageSet: Class to contain pixel-sparse imaging data
iData-method | iSet: Class to contain high-throughput imaging experiment data and metadata
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: Dense mass spectrometry imaging experiments
iData<--method | MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
iData<--method | SImageData: Class containing sparse image data
iData<--method | SIMageSet: Class to contain pixel-sparse imaging data
iData<--method | iSet: Class to contain high-throughput imaging experiment data and metadata
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
image3D-methods | 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 | ImageData: Class containing arrays of imaging data
imageData | ImagingExperiment: Abstract class for imaging experiments
ImageData-class | ImageData: Class containing arrays of imaging data
imageData-method | ImagingExperiment: Abstract class for imaging experiments
imageData-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
imageData-method | iSet: Class to contain high-throughput imaging experiment data and metadata
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: Dense mass spectrometry imaging experiments
imageData<--method | MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
imageData<--method | iSet: Class to contain high-throughput imaging experiment data and metadata
ImageList | ImageList: Abstract image data list
ImageList-class | ImageList: Abstract image data list
imageShape | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
imageShape-method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
imageShape<- | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
imageShape<--method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
ImagingExperiment | ImagingExperiment: Abstract class for imaging experiments
ImagingExperiment-class | ImagingExperiment: Abstract class for imaging experiments
inferno | Objects exported from other packages
initialize-method | Hashmat: Sparse matrix class using lists as hash tables
initialize-method | IAnnotatedDataFrame: Class containing measured variables and their metadata for imaging experiments
initialize-method | ImageData: Class containing arrays of imaging data
initialize-method | MSImageData: Class containing mass spectrometry image data
initialize-method | MSImageProcess: Class containing mass spectral preprocessing information
initialize-method | MSImageSet: Class to contain mass spectrometry imaging experiment data
initialize-method | MassDataFrame: data frame with mass-to-charge ratio metadata
initialize-method | PositionDataFrame: data frame with spatial position metadata
initialize-method | SImageData: Class containing sparse image data
initialize-method | SIMageSet: Class to contain pixel-sparse imaging data
initialize-method | iSet: Class to contain high-throughput imaging experiment data and metadata
inSituChemistry | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
inSituChemistry-method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
inSituChemistry<- | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
inSituChemistry<--method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
instrumentModel | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
instrumentModel-method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
instrumentModel-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
instrumentModel<- | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
instrumentModel<--method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
instrumentModel<--method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
instrumentVendor | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
instrumentVendor-method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
instrumentVendor-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
instrumentVendor<- | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
instrumentVendor<--method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
instrumentVendor<--method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
intensity.colors | Color palettes for imaging
ionizationType | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
ionizationType-method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
ionizationType-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
ionizationType<- | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
ionizationType<--method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
ionizationType<--method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
iSet | iSet: Class to contain high-throughput imaging experiment data and metadata
iSet-class | iSet: Class to contain high-throughput imaging experiment data and metadata

## -- J --

jet.colors | Color palettes for imaging

## -- K --

keys | Hashmat: Sparse matrix class using lists as hash tables
keys-method | Hashmat: Sparse matrix class using lists as hash tables
keys-method | MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
keys<- | Hashmat: Sparse matrix class using lists as hash tables
keys<--method | Hashmat: Sparse matrix class using lists as hash tables
keys<--method | MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments

## -- 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 | ResultSet: Class to contain analysis results for imaging experiments
length-method | XDataFrame: DataFrame with eXtra metadata columns
length-method | iSet: Class to contain high-throughput imaging experiment data and metadata
lightmode | Color palettes for imaging
lineScanDirection | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
lineScanDirection-method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
lineScanDirection-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
lineScanDirection<- | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
lineScanDirection<--method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
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 | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
massAnalyzerType-method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
massAnalyzerType-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
massAnalyzerType<- | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
massAnalyzerType<--method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
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 | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
matrixApplication-method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
matrixApplication-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
matrixApplication<- | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
matrixApplication<--method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
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 | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
MIAPE-Imaging-class | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
modelData | ResultImagingExperiment: Results of statistical analysis of imaging experiments
modelData-method | ResultImagingExperiment: Results of statistical analysis of imaging experiments
modelData-method | ResultSet: Class to contain analysis results for imaging experiments
modelData<- | ResultImagingExperiment: Results of statistical analysis of imaging experiments
modelData<--method | ResultImagingExperiment: Results of statistical analysis of imaging experiments
modelData<--method | ResultSet: Class to contain analysis results for imaging experiments
MSContinuousImagingExperiment | MSContinuousImagingExperiment: Dense mass spectrometry imaging experiments
MSContinuousImagingExperiment-class | MSContinuousImagingExperiment: Dense 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 | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
msiInfo-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
MSImageData | MSImageData: Class containing mass spectrometry image data
MSImageData-class | MSImageData: Class containing mass spectrometry image data
MSImageProcess | MSImageProcess: Class containing mass spectral preprocessing information
MSImageProcess-class | MSImageProcess: Class containing mass spectral preprocessing information
MSImageSet | MSImageSet: Class to contain mass spectrometry imaging experiment data
MSImageSet-class | MSImageSet: Class to contain mass spectrometry imaging experiment data
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: Dense mass spectrometry imaging experiments
MSProcessedImagingExperiment-class | MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
MSProcessedImagingSpectraList | ImageList: Abstract image data list
MSProcessedImagingSpectraList-class | ImageList: Abstract image data list
mutate | Data transformation and summarization
mutate-method | Data transformation and summarization
mz | Manipulate mass-to-charge-ratio values
mz-method | MSImageSet: Class to contain mass spectrometry imaging experiment data
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 | MSImageSet: Class to contain mass spectrometry imaging experiment data
mz<--method | MSImagingExperiment: Mass spectrometry imaging experiments
mz<--method | MSProcessedImagingExperiment: Dense 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: Dense mass spectrometry imaging experiments
mzData-method | MSImageData: Class containing mass spectrometry image data
mzData-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
mzData-method | MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
mzData-method | SImageData: Class containing sparse image data
mzData-methods | MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
mzData<- | MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
mzData<--method | MSImageData: Class containing mass spectrometry image data
mzData<--method | MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
mzData<--method | SImageData: Class containing sparse image data
mzFilter | Peak filter or mass filter an imaging dataset
mzFilter-method | Peak filter or mass filter an imaging dataset
mzFilter-methods | Peak filter or mass filter an imaging dataset

## -- N --

names-method | ImageData: Class containing arrays of imaging data
names-method | ImageList: Abstract image data list
names-method | ResultSet: Class to contain analysis results for imaging experiments
names-method | XDataFrame: DataFrame with eXtra metadata columns
names<--method | ImageData: Class containing arrays of imaging data
names<--method | ImageList: Abstract image data list
normalization | MSImageProcess: Class containing mass spectral preprocessing information
normalization-method | MSImageProcess: Class containing mass spectral preprocessing information
normalization-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
normalization<- | MSImageProcess: Class containing mass spectral preprocessing information
normalization<--method | MSImageProcess: Class containing mass spectral preprocessing information
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
notes-method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
notes<--method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information

## -- O --

OPLS | Partial least squares
OPLS-class | Partial least squares
OPLS-method | Partial least squares
OPLS-methods | Partial least squares
otherInfo-method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information

## -- P --

PCA | Principal components analysis
PCA-class | Principal components analysis
PCA-method | Principal components analysis
PCA-methods | Principal components analysis
pData | ImagingExperiment: Abstract class for imaging experiments
pData-method | Hashmat: Sparse matrix class using lists as hash tables
pData-method | ImagingExperiment: Abstract class for imaging experiments
pData-method | iSet: Class to contain high-throughput imaging experiment data and metadata
pData-methods | ImagingExperiment: Abstract class for imaging experiments
pData<- | ImagingExperiment: Abstract class for imaging experiments
pData<--method | Hashmat: Sparse matrix class using lists as hash tables
pData<--method | ImagingExperiment: Abstract class for imaging experiments
pData<--method | iSet: Class to contain high-throughput imaging experiment data and metadata
peakAlign | Peak align an imaging dataset
peakAlign-method | Peak align an imaging dataset
peakAlign-methods | Peak align an imaging dataset
peakAlign.diff | Peak align an imaging dataset
peakAlign.DP | Peak align an imaging dataset
peakBin | Peak bin an imaging dataset
peakBin-method | Peak bin an imaging dataset
peakBin-methods | Peak bin an imaging dataset
peakData | MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
peakData-method | MSImageData: Class containing mass spectrometry image data
peakData-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
peakData-method | MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
peakData-method | SImageData: Class containing sparse image data
peakData-methods | MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
peakData<- | MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
peakData<--method | MSImageData: Class containing mass spectrometry image data
peakData<--method | MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
peakData<--method | SImageData: Class containing sparse image data
peakFilter | Peak filter or mass filter an imaging dataset
peakFilter-method | Peak filter or mass filter an imaging dataset
peakFilter-methods | Peak filter or mass filter an imaging dataset
peakFilter.freq | Peak filter or mass filter an imaging dataset
peakPick | Peak pick an imaging dataset
peakPick-method | Peak pick an imaging dataset
peakPick-methods | Peak pick an imaging dataset
peakPick.adaptive | Peak pick an imaging dataset
peakPick.limpic | Peak pick an imaging dataset
peakPick.mad | Peak pick an imaging dataset
peakPick.simple | Peak pick an imaging dataset
peakPicking | MSImageProcess: Class containing mass spectral preprocessing information
peakPicking-method | MSImageProcess: Class containing mass spectral preprocessing information
peakPicking-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
peakPicking<- | MSImageProcess: Class containing mass spectral preprocessing information
peakPicking<--method | MSImageProcess: Class containing mass spectral preprocessing information
peakPicking<--method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
peaks | MSImagingExperiment: Mass spectrometry imaging experiments
peaks-method | MSImageSet: Class to contain mass spectrometry imaging experiment data
peaks-method | MSImagingExperiment: Mass spectrometry imaging experiments
peaks-methods | MSImagingExperiment: Mass spectrometry imaging experiments
peaks<- | MSImagingExperiment: Mass spectrometry imaging experiments
peaks<--method | MSImageSet: Class to contain mass spectrometry imaging experiment data
peaks<--method | MSImagingExperiment: Mass spectrometry 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 | iSet: Class to contain high-throughput imaging experiment data and metadata
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 | iSet: Class to contain high-throughput imaging experiment data and metadata
pixelNames | ImagingExperiment: Abstract class for imaging experiments
pixelNames-method | IAnnotatedDataFrame: Class containing measured variables and their metadata for imaging experiments
pixelNames-method | ImagingExperiment: Abstract class for imaging experiments
pixelNames-method | SImageData: Class containing sparse image data
pixelNames-method | iSet: Class to contain high-throughput imaging experiment data and metadata
pixelNames-methods | ImagingExperiment: Abstract class for imaging experiments
pixelNames<- | ImagingExperiment: Abstract class for imaging experiments
pixelNames<--method | IAnnotatedDataFrame: Class containing measured variables and their metadata for imaging experiments
pixelNames<--method | ImagingExperiment: Abstract class for imaging experiments
pixelNames<--method | SImageData: Class containing sparse image data
pixelNames<--method | SIMageSet: Class to contain pixel-sparse imaging data
pixelNames<--method | iSet: Class to contain high-throughput imaging experiment data and metadata
pixels | ImagingExperiment: Abstract class for imaging experiments
pixels-method | ImagingExperiment: Abstract class for imaging experiments
pixels-method | MSImageSet: Class to contain mass spectrometry imaging experiment data
pixels-method | MSImagingExperiment: Mass spectrometry imaging experiments
pixels-method | iSet: Class to contain high-throughput imaging experiment data and metadata
pixels-methods | ImagingExperiment: Abstract class for imaging experiments
pixelSize | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
pixelSize-method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
pixelSize-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
pixelSize<- | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
pixelSize<--method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
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
plot.summary.CrossValidated | Apply cross-validation to imaging analyses
plot.summary.OPLS | Partial least squares
plot.summary.PCA | Principal components analysis
plot.summary.PLS | Partial least squares
plot.summary.SpatialFastmap | Spatially-aware FastMap projection
plot.summary.SpatialKMeans | Spatially-aware k-means clustering
plot.summary.SpatialShrunkenCentroids | Spatially-aware shrunken centroid clustering and classification
PLS | Partial least squares
PLS-class | Partial least squares
PLS-method | Partial least squares
PLS-methods | Partial least squares
positionArray | SImageData: Class containing sparse image data
positionArray-method | SImageData: Class containing sparse image data
positionArray<- | SImageData: Class containing sparse image data
positionArray<--method | SImageData: Class containing sparse image data
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 | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
preproc-method | SparseImagingExperiment: Pixel-sparse imaging experiments
preproc<--method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
presetImageDef | Simulate a mass spectrum or MS imaging experiment
print.summary.CrossValidated | Apply cross-validation to imaging analyses
print.summary.iSet | iSet: Class to contain high-throughput imaging experiment data and metadata
print.summary.OPLS | Partial least squares
print.summary.PCA | Principal components analysis
print.summary.PLS | Partial least squares
print.summary.SpatialFastmap | Spatially-aware FastMap projection
print.summary.SpatialKMeans | Spatially-aware k-means clustering
print.summary.SpatialShrunkenCentroids | Spatially-aware shrunken centroid clustering and classification
process | Delayed Processing of Imaging Datasets
process-method | Delayed Processing of Imaging Datasets
process-methods | Delayed Processing of Imaging Datasets
processingData | MSImageSet: Class to contain mass spectrometry imaging experiment data
processingData-method | MSImageSet: Class to contain mass spectrometry imaging experiment data
processingData-method | SparseImagingExperiment: Pixel-sparse imaging experiments
processingData-methods | MSImageSet: Class to contain mass spectrometry imaging experiment data
processingData<- | MSImageSet: Class to contain mass spectrometry imaging experiment data
processingData<--method | MSImageSet: Class to contain mass spectrometry imaging experiment data
processingData<--method | SparseImagingExperiment: Pixel-sparse imaging experiments
prochistory | MSImageProcess: Class containing mass spectral preprocessing information
prochistory-method | MSImageProcess: Class containing mass spectral preprocessing information
prochistory<- | MSImageProcess: Class containing mass spectral preprocessing information
prochistory<--method | MSImageProcess: Class containing mass spectral preprocessing information
protocolData-method | iSet: Class to contain high-throughput imaging experiment data and metadata
protocolData<--method | iSet: Class to contain high-throughput imaging experiment data and metadata
pubMedIds-method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
pubMedIds<--method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information

## -- R --

rbind-method | Hashmat: Sparse matrix class using lists as hash tables
rbind-method | ImageList: Abstract image data list
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 | ResultImagingExperiment: Results of statistical analysis of imaging experiments
rbind-method | SparseImagingExperiment: Pixel-sparse imaging experiments
rbind-method | XDataFrame: DataFrame with eXtra metadata columns
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
reduceDimension | Reduce the dimension of an imaging dataset
reduceDimension-method | Reduce the dimension of an imaging dataset
reduceDimension-methods | Reduce the dimension of an imaging dataset
reduceDimension.bin | Reduce the dimension of an imaging dataset
reduceDimension.peaks | Reduce the dimension of an imaging dataset
reduceDimension.resample | Reduce the dimension of an imaging dataset
regeneratePositions | SImageData: Class containing sparse image data
regeneratePositions-method | SImageData: Class containing sparse image data
regeneratePositions-method | SIMageSet: Class to contain pixel-sparse imaging data
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<- | PositionDataFrame: data frame with spatial position metadata
resolution<--method | MSImagingExperiment: Mass spectrometry imaging experiments
resolution<--method | MSProcessedImagingExperiment: Dense 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
resultData | ResultImagingExperiment: Results of statistical analysis of imaging experiments
resultData-method | ResultImagingExperiment: Results of statistical analysis of imaging experiments
resultData-method | ResultSet: Class to contain analysis results for imaging experiments
resultData<- | ResultImagingExperiment: Results of statistical analysis of imaging experiments
resultData<--method | ResultImagingExperiment: Results of statistical analysis of imaging experiments
resultData<--method | ResultSet: Class to contain analysis results for imaging experiments
ResultImagingExperiment | ResultImagingExperiment: Results of statistical analysis of imaging experiments
ResultImagingExperiment-class | ResultImagingExperiment: Results of statistical analysis of imaging experiments
resultNames | ResultImagingExperiment: Results of statistical analysis of imaging experiments
resultNames-method | ResultImagingExperiment: Results of statistical analysis of imaging experiments
resultNames<- | ResultImagingExperiment: Results of statistical analysis of imaging experiments
ResultSet | ResultSet: Class to contain analysis results for imaging experiments
ResultSet-class | ResultSet: Class to contain analysis results for imaging experiments
risk.colors | Color palettes for imaging
rownames-method | Hashmat: Sparse matrix class using lists as hash tables
rownames<--method | Hashmat: Sparse matrix class using lists as hash tables
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-method | IAnnotatedDataFrame: Class containing measured variables and their metadata for imaging experiments
sampleNames-method | iSet: Class to contain high-throughput imaging experiment data and metadata
sampleNames<--method | IAnnotatedDataFrame: Class containing measured variables and their metadata for imaging experiments
sampleNames<--method | iSet: Class to contain high-throughput imaging experiment data and metadata
samples-method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanDirection | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanDirection-method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanDirection-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
scanDirection<- | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanDirection<--method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanDirection<--method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
scanPattern | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanPattern-method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanPattern-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
scanPattern<- | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanPattern<--method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanPattern<--method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
scanPolarity | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanPolarity-method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanPolarity-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
scanPolarity<- | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanPolarity<--method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanPolarity<--method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
scans-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
scanType | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanType-method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanType-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
scanType<- | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
scanType<--method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
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
select | Data transformation and summarization
select-method | Defunct functions and methods in Cardinal
select-method | Data transformation and summarization
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
show-method | Hashmat: Sparse matrix class using lists as hash tables
show-method | ImageData: Class containing arrays of imaging data
show-method | ImageList: Abstract image data list
show-method | ImagingExperiment: Abstract class for imaging experiments
show-method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
show-method | MSImageProcess: Class containing mass spectral preprocessing information
show-method | MSImagingExperiment: Mass spectrometry imaging experiments
show-method | ResultImagingExperiment: Results of statistical analysis of imaging experiments
show-method | ResultSet: Class to contain analysis results for imaging experiments
show-method | SparseImagingExperiment: Pixel-sparse imaging experiments
show-method | SummaryDataFrame: DataFrame for object summaries
show-method | XDataFrame: DataFrame with eXtra metadata columns
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 | SImageData: Class containing sparse image data
SImageData-class | SImageData: Class containing sparse image data
SImageSet | SIMageSet: Class to contain pixel-sparse imaging data
SImageSet-class | SIMageSet: Class to contain pixel-sparse imaging data
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
smoothing | MSImageProcess: Class containing mass spectral preprocessing information
smoothing-method | MSImageProcess: Class containing mass spectral preprocessing information
smoothing-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
smoothing<- | MSImageProcess: Class containing mass spectral preprocessing information
smoothing<--method | MSImageProcess: Class containing mass spectral preprocessing information
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
softwareName | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
softwareName-method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
softwareName<- | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
softwareName<--method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
softwareVersion | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
softwareVersion-method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
softwareVersion<- | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
softwareVersion<--method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
SparseImagingExperiment | SparseImagingExperiment: Pixel-sparse imaging experiments
SparseImagingExperiment-class | SparseImagingExperiment: Pixel-sparse imaging experiments
SparseResultImagingExperiment | ResultImagingExperiment: Results of statistical analysis of imaging experiments
SparseResultImagingExperiment-class | ResultImagingExperiment: Results of statistical analysis of imaging experiments
spatialApply | Apply functions over imaging datasets
spatialApply-method | Apply functions over imaging datasets
spatialApply-methods | Apply functions over imaging datasets
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
specimenOrigin | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
specimenOrigin-method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
specimenOrigin<- | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
specimenOrigin<--method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
specimenType | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
specimenType-method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
specimenType<- | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
specimenType<--method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
spectra | MSImagingExperiment: Mass spectrometry imaging experiments
spectra-method | MSImageSet: Class to contain mass spectrometry imaging experiment data
spectra-method | MSImagingExperiment: Mass spectrometry imaging experiments
spectra-methods | MSImagingExperiment: Mass spectrometry imaging experiments
spectra<- | MSImagingExperiment: Mass spectrometry imaging experiments
spectra<--method | MSImageSet: Class to contain mass spectrometry imaging experiment data
spectra<--method | MSImagingExperiment: Mass spectrometry imaging experiments
spectrumRepresentation | MSImageProcess: Class containing mass spectral preprocessing information
spectrumRepresentation-method | MSImageProcess: Class containing mass spectral preprocessing information
spectrumRepresentation-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
spectrumRepresentation<- | MSImageProcess: Class containing mass spectral preprocessing information
spectrumRepresentation<--method | MSImageProcess: Class containing mass spectral preprocessing information
spectrumRepresentation<--method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion
stainingMethod | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
stainingMethod-method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
stainingMethod<- | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
stainingMethod<--method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
standardizeRuns | Standardize between runs in an imaging dataset
standardizeRuns-method | Standardize between runs in an imaging dataset
standardizeRuns-methods | Standardize between runs in an imaging dataset
standardizeRuns.sum | Standardize between runs in an imaging dataset
standardizeSamples | Defunct functions and methods in Cardinal
storageMode-method | ImageData: Class containing arrays of imaging data
storageMode-method | iSet: Class to contain high-throughput imaging experiment data and metadata
storageMode<--method | ImageData: Class containing arrays of imaging data
storageMode<--method | iSet: Class to contain high-throughput imaging experiment data and metadata
summarize | Data transformation and summarization
summarize-method | Data transformation and summarization
summary-method | Principal components analysis
summary-method | Partial least squares
summary-method | SummaryDataFrame: DataFrame for object summaries
summary-method | Apply cross-validation to imaging analyses
summary-method | iSet: Class to contain high-throughput imaging experiment data and metadata
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
SummaryDataFrame | SummaryDataFrame: DataFrame for object summaries
SummaryDataFrame-class | SummaryDataFrame: DataFrame for object summaries

## -- T --

tissueThickness | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
tissueThickness-method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
tissueThickness<- | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
tissueThickness<--method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
tissueWash | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
tissueWash-method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
tissueWash<- | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
tissueWash<--method | MIAPE-Imaging: Class for storing mass spectrometry imaging experiment information
tolerance-method | MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
tolerance<--method | MSProcessedImagingExperiment: Dense 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
topLabels | Deprecated functions and methods in Cardinal
topLabels-method | Deprecated functions and methods in Cardinal

## -- U --

ungroup | Objects exported from other packages
ungroup-method | Data transformation and summarization

## -- V --

varLabels-method | iSet: Class to contain high-throughput imaging experiment data and metadata
varLabels<--method | iSet: Class to contain high-throughput imaging experiment data and metadata
varMetadata-method | iSet: Class to contain high-throughput imaging experiment data and metadata
varMetadata<--method | iSet: Class to contain high-throughput imaging experiment data and metadata
viridis | Objects exported from other packages

## -- 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
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 | ResultImagingExperiment: Results of statistical analysis of imaging experiments
$-method | ResultSet: Class to contain analysis results for imaging experiments
$-method | iSet: Class to contain high-throughput imaging experiment data and metadata
$<--method | ImagingExperiment: Abstract class for imaging experiments
$<--method | XDataFrame: DataFrame with eXtra metadata columns
$<--method | iSet: Class to contain high-throughput imaging experiment data and metadata
%>% | Objects exported from other packages
[-method | Hashmat: Sparse matrix class using lists as hash tables
[-method | IAnnotatedDataFrame: Class containing measured variables and their metadata for imaging experiments
[-method | ImageList: Abstract image data list
[-method | MSContinuousImagingExperiment: Dense mass spectrometry imaging experiments
[-method | MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
[-method | MassDataFrame: data frame with mass-to-charge ratio metadata
[-method | PositionDataFrame: data frame with spatial position metadata
[-method | ResultImagingExperiment: Results of statistical analysis of imaging experiments
[-method | ResultSet: Class to contain analysis results for imaging experiments
[-method | SImageData: Class containing sparse image data
[-method | SIMageSet: Class to contain pixel-sparse imaging data
[-method | SparseImagingExperiment: Pixel-sparse imaging experiments
[-method | XDataFrame: DataFrame with eXtra metadata columns
[<--method | Hashmat: Sparse matrix class using lists as hash tables
[<--method | ImageList: Abstract image data list
[<--method | SparseImagingExperiment: Pixel-sparse imaging experiments
[[-method | ImageData: Class containing arrays of imaging data
[[-method | ImageList: Abstract image data list
[[-method | ImagingExperiment: Abstract class for imaging experiments
[[-method | ResultImagingExperiment: Results of statistical analysis of imaging experiments
[[-method | ResultSet: Class to contain analysis results for imaging experiments
[[-method | iSet: Class to contain high-throughput imaging experiment data and metadata
[[<--method | ImageData: Class containing arrays of imaging data
[[<--method | ImageList: Abstract image data list
[[<--method | ImagingExperiment: Abstract class for imaging experiments
[[<--method | MSContinuousImagingExperiment: Dense mass spectrometry imaging experiments
[[<--method | MSProcessedImagingExperiment: Dense mass spectrometry imaging experiments
[[<--method | ResultImagingExperiment: Results of statistical analysis of imaging experiments
[[<--method | XDataFrame: DataFrame with eXtra metadata columns
[[<--method | iSet: Class to contain high-throughput imaging experiment data and metadata