Cardinal
A mass spectrometry imaging toolbox for statistical analysis

Package index
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Vignettes
Functions
1551
Source code
154
Man pages
52
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Cardinal: A mass spectrometry imaging toolbox for statistical analysis
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API

API for Cardinal
A mass spectrometry imaging toolbox for statistical analysis

Global functions
$,ImagingExperiment-method Man page
$,ImagingResult-method Man page
$,ResultSet-method Man page
$,iSet-method Man page
$<-,ImagingExperiment-method Man page
$<-,XDataFrame-method Man page
$<-,iSet-method Man page
%>% Man page
.Deprecated_Cardinal1 Source code
.DollarNames.ImagingExperiment Source code
.DollarNames.ImagingResult Source code
.OPLS.fit Source code
.OPLS.predict Source code
.PCA.fit Source code
.PCA.predict Source code
.PCA2_fit Source code
.PCA2_predict Source code
.PLS.fit Source code
.PLS.predict Source code
.PLS2_fit Source code
.PLS2_predict Source code
.aggregate_funs Source code
.aggregate_stats Source code
.apply Source code
.auto.layout Source code
.bindAnnotatedImageList Source code
.bindImageArrays Source code
.bindSimpleImageArrayList Source code
.bind_dfs_as_list Source code
.calculateClassProbabilities Source code
.calculateFeaturewiseWCSS Source code
.calculateImageValues Source code
.calculatePlotValues Source code
.calculateSpatialDiscriminantScores Source code
.calculateWithinClassPooledSD Source code
.calculateWithinClassPooledSE Source code
.cbind_and_reorder Source code
.checkForIncompleteProcessing Source code
.coerce_ImagingResult Source code
.collect_keyval_pairs Source code
.console Source code
.coregisterCenters Source code
.cv_collate Source code
.cv_simplify Source code
.delayedBatchProcess Source code
.detectMassRangeAndResolution Source code
.distanceFun Source code
.do_dot_expr Source code
.draw.colorkey Source code
.draw.key Source code
.draw.strip.labels Source code
.estimateMassResolution Source code
.estimateNoiseAdaptive Source code
.estimateNoiseMAD Source code
.estimateNoiseSimple Source code
.estimateSpatialResolution Source code
.factor_matrix Source code
.fastFeatureApply Source code
.fastFeatureApply2 Source code
.fastPixelApply Source code
.fastPixelApply2 Source code
.findDistantObjects Source code
.findDistantObjects2 Source code
.findNeighbors Source code
.findSpatialBlocks Source code
.format.data.labels Source code
.format.mz Source code
.format.numbered Source code
.format.plot.label Source code
.formula_feature_results Source code
.formula_pixel_results Source code
.gaussianWeights Source code
.get.MSContinuousImagingInfo Source code
.get.MSProcessedImagingInfo Source code
.getDimsFromResolution Source code
.history Source code
.isCentroided Source code
.locator Source code
.log Source code
.log.collapse Source code
.log.flush Source code
.logProcess Source code
.make.rownames Source code
.make.scanList Source code
.makeAnalyzeHDR Source code
.matchFunOrNULL Source code
.meansTest_LRT Source code
.meansTest_testdata Source code
.meansTest_withmeans Source code
.message Source code
.new.MSContinuousImagingInfo Source code
.new.MSProcessedImagingInfo Source code
.next.figure Source code
.num.panels Source code
.onAttach Source code
.onLoad Source code
.parseFormula Source code
.parseFormula2 Source code
.parseImageFormula Source code
.parsePlotFormula Source code
.parseSide Source code
.parseSide2 Source code
.pendingQueue Source code
.plot.accuracy.factor Source code
.plot.accuracy.numeric Source code
.plot.gridsearch Source code
.protectNestedBPPARAM Source code
.rbind_and_reorder Source code
.readAnalyzeHDR Source code
.readAnalyzeIMG Source code
.readAnalyzeT2M Source code
.readIbd Source code
.readImzML Source code
.remote_collect Source code
.remote_writer Source code
.replaceSimpleImageArrayList Source code
.reshape_feature_results Source code
.reshape_pixel_results Source code
.scat Source code
.segmentationTest_getclasses Source code
.segmentationTest_testdata Source code
.segmentationTest_withmeans Source code
.selectPixels Source code
.selectROI Source code
.selectRegion Source code
.session Source code
.setResolutionfromCoord Source code
.setResolutionfromMass Source code
.setup.layout Source code
.show.ImagingResult Source code
.simulateSpectrum Source code
.spaste Source code
.spatialDGMM_Estep Source code
.spatialDGMM_Mstep Source code
.spatialDGMM_cluster Source code
.spatialDGMM_collate Source code
.spatialDGMM_fit1 Source code
.spatialDGMM_withmeans Source code
.spatialDistance Source code
.spatialDistance2 Source code
.spatialDistanceFun Source code
.spatialFastmap Source code
.spatialFastmap2 Source code
.spatialFilter Source code
.spatialInfo Source code
.spatialKMeans Source code
.spatialKMeans.reclass Source code
.spatialKMeans2 Source code
.spatialOffsets Source code
.spatialScores Source code
.spatialShrunkenCentroids.cluster Source code
.spatialShrunkenCentroids.fit Source code
.spatialShrunkenCentroids.predict Source code
.spatialShrunkenCentroids.reclass Source code
.spatialShrunkenCentroids2_cluster Source code
.spatialShrunkenCentroids2_fit Source code
.spatialShrunkenCentroids2_predict Source code
.spatialWeights Source code
.stop Source code
.subsetAnnotatedImageList Source code
.subsetSimpleImageArrayList Source code
.summarize.factor Source code
.summarize.numeric Source code
.summarize_expr Source code
.summarize_stat Source code
.tapply Source code
.templateImzML Source code
.time.start Source code
.time.stop Source code
.to_MSContinuousImagingSpectraList Source code
.to_MSProcessedImagingSpectraList Source code
.try_eval Source code
.unlist_and_reorder Source code
.unlist_once Source code
.update.par Source code
.valid.AnnotatedImage Source code
.valid.AnnotatedImageList Source code
.valid.AnnotatedImagingExperiment Source code
.valid.ImageArrayList Source code
.valid.ImageList Source code
.valid.ImagingResult Source code
.valid.MSContinuousImagingSpectraList Source code
.valid.MSImagingInfo Source code
.valid.MSProcessedImagingSpectraList Source code
.valid.MassDataFrame Source code
.valid.PositionDataFrame Source code
.valid.SparseImagingExperiment Source code
.virtual.image Source code
.warning Source code
.whichSpatialBlocks Source code
.writeAnalyzeHDR Source code
.writeAnalyzeIMG Source code
.writeAnalyzeT2M Source code
.writeIbd Source code
.writeImzML Source code
AnnotatedImage Man page Source code
AnnotatedImage-class Man page
AnnotatedImageList Man page Source code
AnnotatedImageList-class Man page
AnnotatedImagingExperiment Man page Source code
AnnotatedImagingExperiment-class Man page
Cardinal Man page
Cardinal-internal Man page
Cardinal-legacy Man page
Cardinal-package Man page
Cardinal-reexports Man page
CardinalLog Man page Source code
CardinalVersion Man page Source code
Csizeof Source code
Ctypeof Source code
Defunct Man page
Deprecated Man page
Hashmat Man page Source code
Hashmat-class Man page
IAnnotatedDataFrame Man page Source code
IAnnotatedDataFrame-class Man page
ImageArrayList Man page Source code
ImageArrayList-class Man page
ImageData Man page Source code
ImageData-class Man page
ImageList Man page Source code
ImageList-class Man page
ImagingExperiment Man page
ImagingExperiment-class Man page
ImagingResult Man page
ImagingResult-class Man page
MIAPE-Imaging Man page
MIAPE-Imaging-class Man page
MSContinuousImagingExperiment Man page
MSContinuousImagingExperiment-class Man page
MSContinuousImagingSpectraList Man page Source code
MSContinuousImagingSpectraList-class Man page
MSImageData Man page Source code
MSImageData-class Man page
MSImageProcess Man page
MSImageProcess-class Man page
MSImageSet Man page Source code
MSImageSet-class Man page
MSImagingExperiment Man page Source code
MSImagingExperiment-class Man page
MSImagingInfo Man page
MSImagingInfo-class Man page
MSProcessedImagingExperiment Man page
MSProcessedImagingExperiment-class Man page
MSProcessedImagingSpectraList Man page Source code
MSProcessedImagingSpectraList-class Man page
MassDataFrame Man page Source code
MassDataFrame-class Man page
MeansTest-class Man page
Mode Source code
Mscore Source code
Nametypeof Source code
OPLS Man page
OPLS,SImageSet,ANY-method Man page
OPLS,SImageSet,matrix-method Man page
OPLS,SparseImagingExperiment,ANY-method Man page
OPLS-class Man page
OPLS-methods Man page
PCA Man page
PCA,SImageSet-method Man page
PCA,SparseImagingExperiment-method Man page
PCA-class Man page
PCA-methods Man page
PLS Man page
PLS,SImageSet,ANY-method Man page
PLS,SImageSet,matrix-method Man page
PLS,SparseImagingExperiment,ANY-method Man page
PLS-class Man page
PLS-methods Man page
PositionDataFrame Man page Source code
PositionDataFrame-class Man page
ResultSet Man page
ResultSet-class Man page
SImageData Man page Source code
SImageData-class Man page
SImageSet Man page Source code
SImageSet-class Man page
SegmentationTest-class Man page
SimpleImageArrayList-class Man page
SimpleImageList-class Man page
SparseImagingExperiment Man page Source code
SparseImagingExperiment-class Man page
SparseImagingResult Man page
SparseImagingResult-class Man page
SpatialDGMM-class Man page
SpatialKMeans-class Man page
SpatialShrunkenCentroids-class Man page
SummaryDataFrame Man page Source code
SummaryDataFrame-class Man page
XDataFrame Man page Source code
XDataFrame-class Man page
[,AnnotatedImageList,ANY,ANY,ANY-method Man page
[,Hashmat,ANY,ANY,ANY-method Man page
[,Hashmat,ANY,ANY,NULL-method Man page
[,Hashmat-method Man page
[,IAnnotatedDataFrame,ANY,ANY,ANY-method Man page
[,ImageArrayList,ANY,ANY,ANY-method Man page
[,ImageArrayList-method Man page Man page
[,ImagingExperiment,ANY,ANY,ANY-method Man page
[,MSContinuousImagingSpectraList,ANY,ANY,ANY-method Man page
[,MSProcessedImagingSpectraList,ANY,ANY,ANY-method Man page
[,MassDataFrame,ANY,ANY,ANY-method Man page
[,PositionDataFrame,ANY,ANY,ANY-method Man page
[,ResultSet,ANY,ANY,ANY-method Man page
[,ResultSet-method Man page
[,SImageData,ANY,ANY,ANY-method Man page
[,SImageData,ANY,ANY,NULL-method Man page
[,SImageData-method Man page
[,SImageSet,ANY,ANY,ANY-method Man page
[,SImageSet-method Man page
[,SparseImagingExperiment,ANY,ANY,ANY-method Man page
[,SparseImagingResult,ANY,ANY,ANY-method Man page
[,XDataFrame,ANY,ANY,ANY-method Man page
[<-,Hashmat,ANY,ANY,ANY-method Man page
[<-,Hashmat-method Man page
[<-,ImageArrayList,ANY,ANY,ANY-method Man page
[<-,ImagingExperiment,ANY,ANY,ANY-method Man page
[<-,SparseImagingExperiment,ANY,ANY,ANY-method Man page
[[,ImageData,character,missing-method Man page
[[,ImageData-method Man page
[[,ImageList,ANY,ANY-method Man page
[[,ImagingExperiment,ANY,ANY-method Man page
[[,ImagingResult,ANY,ANY-method Man page
[[,ResultSet,ANY,ANY-method Man page
[[,ResultSet-method Man page
[[,SparseImagingResult,ANY,ANY-method Man page
[[,iSet,ANY,ANY-method Man page
[[,iSet-method Man page
[[<-,ImageData,character,missing-method Man page
[[<-,ImageData-method Man page
[[<-,ImageList,ANY,ANY-method Man page
[[<-,ImagingExperiment,ANY,ANY-method Man page
[[<-,ImagingResult,ANY,ANY-method Man page
[[<-,MSContinuousImagingSpectraList,ANY,ANY-method Man page
[[<-,MSProcessedImagingSpectraList,ANY,ANY-method Man page
[[<-,SparseImagingResult,ANY,ANY-method Man page
[[<-,XDataFrame,ANY,ANY-method Man page
[[<-,iSet,ANY,ANY-method Man page
[[<-,iSet-method Man page
abstract,MIAPE-Imaging-method Man page
addShape Man page Source code
affine Source code
aggregate,MSImagingExperiment-method Man page
aggregate,SparseImagingExperiment-method Man page
allmissing Source code
alpha.colors Man page Source code
annotatedDataFrameFrom,ImageData-method Man page
arrange Man page
arrange.DataFrame Source code
arrange.SummaryDataFrame Source code
arrange.XDataFrame Source code
as.data.frame,XDataFrame-method Man page
as.env,XDataFrame-method Man page
as.env,list-method Man page
as.list,ImageList-method Man page
as.list,MSImagingInfo-method Man page
as.list,MassDataFrame-method Man page
as.list,PositionDataFrame-method Man page
as.matrix,XDataFrame-method Man page
baselineReduction Man page
baselineReduction,MSImageProcess-method Man page
baselineReduction,Vector-method Man page
baselineReduction<- Man page
baselineReduction<-,MSImageProcess-method Man page
baselineReduction<-,Vector-method Man page
batch.args Source code
batchProcess Man page
batchProcess,MSImageSet-method Man page
batchProcess-methods Man page
bisection.seq Source code
bw.colors Man page Source code
cbind,AnnotatedImageList-method Man page
cbind,Hashmat-method Man page
cbind,ImageArrayList-method Man page
cbind,ImagingExperiment-method Man page
cbind,MSImagingExperiment-method Man page
cbind,MassDataFrame-method Man page
cbind,PositionDataFrame-method Man page
cbind,SparseImagingExperiment-method Man page
cbind,SparseImagingResult-method Man page
cbind,XDataFrame-method Man page
cbrt Source code
centroided Man page
centroided,MSImageProcess-method Man page
centroided,MSImageSet-method Man page
centroided,MSImagingExperiment-method Man page
centroided<- Man page
centroided<-,MSImageProcess-method Man page
centroided<-,MSImageSet-method Man page
centroided<-,MSImagingExperiment-method Man page
cividis Man page
class:AnnotatedImage Man page
class:AnnotatedImageList Man page
class:AnnotatedImagingExperiment Man page
class:Hashmat Man page
class:IAnnotatedDataFrame Man page
class:ImageArrayList Man page
class:ImageData Man page
class:ImageList Man page
class:ImagingExperiment Man page
class:ImagingResult Man page
class:MIAPE-Imaging Man page
class:MSContinuousImagingExperiment Man page
class:MSContinuousImagingSpectraList Man page
class:MSImageData Man page
class:MSImageProcess Man page
class:MSImageSet Man page
class:MSImagingExperiment Man page
class:MSImagingInfo Man page
class:MSProcessedImagingExperiment Man page
class:MSProcessedImagingSpectraList Man page
class:MassDataFrame Man page
class:MeansTest Man page
class:OPLS Man page
class:PCA Man page
class:PLS Man page
class:PositionDataFrame Man page
class:ResultSet Man page
class:SImageData Man page
class:SImageSet Man page
class:SegmentationTest Man page
class:SimpleImageArrayList Man page
class:SimpleImageList Man page
class:SparseImagingExperiment Man page
class:SparseImagingResult Man page
class:SpatialDGMM Man page
class:SpatialKMeans Man page
class:SpatialShrunkenCentroids Man page
class:SummaryDataFrame Man page
class:XDataFrame Man page
class:iSet Man page
class:spatialFastmap Man page
col.map Man page Source code
collect Man page
collect.MSImagingExperiment Man page Source code
collect.MSProcessedImagingExperiment Man page Source code
collect.SparseImagingExperiment Man page Source code
colnames,Hashmat-method Man page
colnames<-,Hashmat-method Man page
colocalized Man page
colocalized,MSImagingExperiment,missing-method Man page
colocalized,SparseImagingExperiment,ANY-method Man page
colocalized,SpatialDGMM,ANY-method Man page
color.map Man page Source code
combine,AnnotatedImageList,ANY-method Man page
combine,Hashmat,Hashmat-method Man page
combine,IAnnotatedDataFrame,IAnnotatedDataFrame-method Man page
combine,ImageData,ImageData-method Man page
combine,ImagingExperiment,ANY-method Man page
combine,MIAPE-Imaging,MIAPE-Imaging-method Man page
combine,MSImageProcess,MSImageProcess-method Man page
combine,MSImageSet,MSImageSet-method Man page
combine,SImageData,SImageData-method Man page
combine,SImageSet,SImageSet-method Man page
combine,SparseImagingExperiment,ANY-method Man page
combine,SparseImagingResult,ANY-method Man page
combine,array,array-method Man page
combine,iSet,iSet-method Man page
combine,vector,vector-method Man page
combinedMean Source code
combinedVar Source code
combiner,MSProcessedImagingExperiment-method Man page
combiner,MSProcessedImagingSpectraList-method Man page
combiner<-,MSProcessedImagingExperiment-method Man page
combiner<-,MSProcessedImagingSpectraList-method Man page
contrast.enhance.histogram Source code
contrast.enhance.method Source code
contrast.enhance.suppression Source code
coord Man page
coord,AnnotatedImage-method Man page
coord,AnnotatedImagingExperiment-method Man page
coord,IAnnotatedDataFrame-method Man page
coord,PositionDataFrame-method Man page
coord,SImageData-method Man page
coord,SparseImagingExperiment-method Man page
coord,iSet-method Man page
coord-methods Man page
coord<- Man page
coord<-,AnnotatedImage-method Man page
coord<-,IAnnotatedDataFrame-method Man page
coord<-,PositionDataFrame-method Man page
coord<-,SImageData-method Man page
coord<-,SImageSet-method Man page
coord<-,SparseImagingExperiment-method Man page
coord<-,iSet-method Man page
coordLabels Man page
coordLabels,IAnnotatedDataFrame-method Man page
coordLabels,PositionDataFrame-method Man page
coordLabels,SparseImagingExperiment-method Man page
coordLabels,iSet-method Man page
coordLabels-methods Man page
coordLabels<- Man page
coordLabels<-,IAnnotatedDataFrame-method Man page
coordLabels<-,PositionDataFrame-method Man page
coordLabels<-,SImageSet-method Man page
coordLabels<-,SparseImagingExperiment-method Man page
coordLabels<-,iSet-method Man page
coordinates Man page
coordinates,AnnotatedImage-method Man page
coordinates,AnnotatedImagingExperiment-method Man page
coordinates,PositionDataFrame-method Man page
coordinates,SparseImagingExperiment-method Man page
coordinates-methods Man page
coordinates<- Man page
coordinates<-,AnnotatedImage-method Man page
coordinates<-,PositionDataFrame-method Man page
coordinates<-,SparseImagingExperiment-method Man page
coordnames Man page
coordnames,PositionDataFrame-method Man page
coordnames,SparseImagingExperiment-method Man page
coordnames-methods Man page
coordnames<- Man page
coordnames<-,PositionDataFrame,ANY-method Man page
coordnames<-,SparseImagingExperiment,ANY-method Man page
coregister Man page
coregister,SpatialKMeans,missing-method Man page
coregister,SpatialShrunkenCentroids,missing-method Man page
coregister-methods Man page
crossValidate Man page
crossValidate,MSImagingExperiment-method Man page
crossValidate,SparseImagingExperiment-method Man page
crossValidate-methods Man page
cvApply Man page
cvApply,SImageSet-method Man page
cvApply,SparseImagingExperiment-method Man page
cvApply-methods Man page
darkmode Man page Source code
diffAlign Source code
dim,AnnotatedImageList-method Man page
dim,Hashmat-method Man page
dim,ImageData-method Man page
dim,ImageList-method Man page
dim,ImagingExperiment-method Man page
dim,SImageData-method Man page
dim,SparseImagingExperiment-method Man page
dim,iSet-method Man page
dim<-,Hashmat-method Man page
dimnames,Hashmat-method Man page
dimnames,ImagingExperiment-method Man page
dimnames<-,Hashmat,ANY-method Man page
dimnames<-,Hashmat-method Man page
dims,AnnotatedImageList-method Man page
dims,AnnotatedImagingExperiment-method Man page
dims,ImageData-method Man page
dims,ImageList-method Man page
dims,PositionDataFrame-method Man page
dims,SImageData-method Man page
dims,SparseImagingExperiment-method Man page
dims,iSet-method Man page
discrete.colors Man page Source code
divergent.colors Man page Source code
dynamicAlign Source code
embeddingMethod Man page
embeddingMethod,MIAPE-Imaging-method Man page
experimentData,iSet-method Man page
experimentData<-,iSet,ANY-method Man page
expinfo,MIAPE-Imaging-method Man page
fData Man page
fData,ImagingExperiment-method Man page
fData,iSet-method Man page
fData-methods Man page
fData<- Man page
fData<-,ImagingExperiment,ANY-method Man page
fData<-,iSet,ANY-method Man page
fData<-,iSet-method Man page
facet.boxplot Source code
facet.count Source code
facet.image Source code
facet.plot Source code
facet.raster Source code
fastmap Source code
featureApply Man page
featureApply,SImageSet-method Man page
featureApply,SparseImagingExperiment-method Man page
featureApply-methods Man page
featureData Man page
featureData,ImagingExperiment-method Man page
featureData,iSet-method Man page
featureData-methods Man page
featureData<- Man page
featureData<-,ImagingExperiment,ANY-method Man page
featureData<-,ImagingExperiment-method Man page
featureData<-,iSet,ANY-method Man page
featureData<-,iSet-method Man page
featureNames Man page
featureNames,ImagingExperiment-method Man page
featureNames,SImageData-method Man page
featureNames,iSet-method Man page
featureNames-methods Man page
featureNames<- Man page
featureNames<-,ImagingExperiment-method Man page
featureNames<-,SImageData-method Man page
featureNames<-,SImageSet-method Man page
featureNames<-,iSet-method Man page
features Man page
features,MSImageSet-method Man page
features,MSImagingExperiment-method Man page
features,SparseImagingExperiment-method Man page
features,iSet-method Man page
features-methods Man page
file_ext Source code
file_path_sans_ext Source code
filter Man page
filter.DataFrame Source code
filter.SparseImagingExperiment Man page Source code
filter.SummaryDataFrame Source code
filter.XDataFrame Source code
findNeighbors Man page
findNeighbors,IAnnotatedDataFrame-method Man page
findNeighbors,ImagingExperiment-method Man page
findNeighbors,PositionDataFrame-method Man page
findNeighbors,iSet-method Man page
findNeighbors-methods Man page
fitted,PLS2-method Man page
fitted,SpatialShrunkenCentroids2-method Man page
fvarLabels,iSet-method Man page
fvarLabels<-,iSet-method Man page
fvarMetadata,iSet-method Man page
fvarMetadata<-,iSet,ANY-method Man page
fvarMetadata<-,iSet-method Man page
generateImage Man page Source code
generatePositionArray Source code
generateRNGStreams Source code
generateSpectrum Man page Source code
getCardinalBPPARAM Man page Source code
getCardinalDelayProc Man page Source code
getCardinalNumBlocks Man page Source code
getCardinalVerbose Man page Source code
getRNGStream Source code
gradient.colors Man page Source code
gridded,PositionDataFrame-method Man page
gridded,SparseImagingExperiment-method Man page
gridded<-,PositionDataFrame,ANY-method Man page
gridded<-,SparseImagingExperiment,ANY-method Man page
groupMean Source code
groupVar Source code
group_by Man page
group_by.DataFrame Source code
group_by.XDataFrame Source code
groups Man page
groups.XDataFrame Source code
height Man page
height,AnnotatedImage-method Man page
height,AnnotatedImagingExperiment-method Man page
height<- Man page
height<-,AnnotatedImage-method Man page
iData Man page
iData,ImagingExperiment,ANY-method Man page
iData,ImagingExperiment,missing-method Man page
iData,SImageData,ANY-method Man page
iData,SImageSet,ANY-method Man page
iData,iSet-method Man page
iData-methods Man page
iData<- Man page
iData<-,ImagingExperiment,ANY-method Man page
iData<-,ImagingExperiment,missing-method Man page
iData<-,MSContinuousImagingExperiment,ANY-method Man page
iData<-,MSContinuousImagingExperiment,missing-method Man page
iData<-,MSProcessedImagingExperiment,ANY-method Man page
iData<-,MSProcessedImagingExperiment,missing-method Man page
iData<-,SImageData,ANY-method Man page
iData<-,SImageSet,ANY-method Man page
iData<-,iSet-method Man page
iSet Man page
iSet-class Man page
image Man page
image,AnnotatedImage-method Man page
image,AnnotatedImageList-method Man page
image,AnnotatedImagingExperiment-method Man page
image,CrossValidated-method Man page
image,MSImageSet-method Man page
image,MSImagingExperiment-method Man page
image,MSImagingSummary-method Man page
image,MeansTest-method Man page
image,OPLS-method Man page
image,PCA-method Man page
image,PCA2-method Man page
image,PLS-method Man page
image,PLS2-method Man page
image,PositionDataFrame-method Man page
image,ResultSet-method Man page
image,SImageSet-method Man page
image,SegmentationTest-method Man page
image,SparseImagingExperiment-method Man page
image,SparseImagingResult-method Man page
image,SparseImagingSummary-method Man page
image,SpatialDGMM-method Man page
image,SpatialFastmap-method Man page
image,SpatialFastmap2-method Man page
image,SpatialKMeans-method Man page
image,SpatialKMeans2-method Man page
image,SpatialShrunkenCentroids-method Man page
image,SpatialShrunkenCentroids2-method Man page
image,formula-method Man page
image-methods Man page
image3D Man page
image3D,CrossValidated-method Man page
image3D,MSImageSet-method Man page
image3D,MeansTest-method Man page
image3D,OPLS-method Man page
image3D,PCA-method Man page
image3D,PCA2-method Man page
image3D,PLS-method Man page
image3D,PLS2-method Man page
image3D,ResultSet-method Man page
image3D,SImageSet-method Man page
image3D,SegmentationTest-method Man page
image3D,SparseImagingExperiment-method Man page
image3D,SpatialDGMM-method Man page
image3D,SpatialFastmap-method Man page
image3D,SpatialFastmap2-method Man page
image3D,SpatialKMeans-method Man page
image3D,SpatialKMeans2-method Man page
image3D,SpatialShrunkenCentroids-method Man page
image3D,SpatialShrunkenCentroids2-method Man page
image3D-methods Man page
image3d Source code
imageData Man page
imageData,ImagingExperiment-method Man page
imageData,iSet-method Man page
imageData-methods Man page
imageData<- Man page
imageData<-,ImagingExperiment-method Man page
imageData<-,MSContinuousImagingExperiment-method Man page
imageData<-,MSProcessedImagingExperiment-method Man page
imageData<-,iSet-method Man page
imageShape Man page
imageShape,MIAPE-Imaging-method Man page
inSituChemistry Man page
inSituChemistry,MIAPE-Imaging-method Man page
inferno Man page
initialize,Hashmat-method Man page
initialize,IAnnotatedDataFrame-method Man page
initialize,ImageData-method Man page
initialize,MSImageData-method Man page
initialize,MSImageProcess-method Man page
initialize,MSImageSet-method Man page
initialize,MassDataFrame-method Man page
initialize,PositionDataFrame-method Man page
initialize,SImageData-method Man page
initialize,SImageSet-method Man page
initialize,iSet-method Man page
instrumentModel Man page
instrumentModel,MIAPE-Imaging-method Man page
instrumentModel,Vector-method Man page
instrumentVendor Man page
instrumentVendor,MIAPE-Imaging-method Man page
instrumentVendor,Vector-method Man page
intensity.colors Man page Source code
intensity.colors2 Source code
intensityData Man page
intensityData,MSImagingInfo-method Man page
intensityData,MSProcessedImagingExperiment-method Man page
intensityData-methods Man page
intensityData<- Man page
intensityData<-,MSProcessedImagingExperiment-method Man page
interpolate.bilinear Source code
ionizationType Man page
ionizationType,MIAPE-Imaging-method Man page
ionizationType,Vector-method Man page
is.discrete Source code
is.max Source code
is.min Source code
is.numeric_vector Source code
is.wholenumber Source code
is3D Man page
is3D,IAnnotatedDataFrame-method Man page
is3D,PositionDataFrame-method Man page
is3D,SImageSet-method Man page
is3D,SparseImagingExperiment-method Man page
isCentroided Man page
isCentroided,MSImagingExperiment-method Man page
isCentroided,MSImagingInfo-method Man page
isCentroided,MassDataFrame-method Man page
is_Analyze_ext Source code
is_imzML_ext Source code
jet.colors Man page Source code
keys Man page
keys,Hashmat-method Man page
keys,MSProcessedImagingSpectraList-method Man page
keys<- Man page
keys<-,Hashmat,character-method Man page
keys<-,Hashmat,list-method Man page
keys<-,Hashmat-method Man page
keys<-,MSProcessedImagingSpectraList,ANY-method Man page
kurtosis Source code
l1norm Source code
l2norm Source code
lapply,XDataFrame-method Man page
length,AnnotatedImage-method Man page
length,ImageList-method Man page
length,ImagingExperiment-method Man page
length,MSImagingInfo-method Man page
length,ResultSet-method Man page
length,XDataFrame-method Man page
length,iSet-method Man page
lightmode Man page Source code
lineScanDirection Man page
lineScanDirection,MIAPE-Imaging-method Man page
lineScanDirection,Vector-method Man page
logLik,SpatialShrunkenCentroids-method Man page
logLik,SpatialShrunkenCentroids2-method Man page
magma Man page
make.annotation Source code
make.uuid Source code
makeFactor Man page Source code
massAnalyzerType Man page
massAnalyzerType,MIAPE-Imaging-method Man page
massAnalyzerType,Vector-method Man page
match.method Source code
matrixApplication Man page
matrixApplication,MIAPE-Imaging-method Man page
matrixApplication,Vector-method Man page
meansTest Man page
meansTest,SparseImagingExperiment-method Man page
meansTest-methods Man page
modelData Man page
modelData,ImagingResult-method Man page
modelData,ResultSet-method Man page
modelData<- Man page
modelData<-,ImagingResult-method Man page
modelData<-,ResultSet-method Man page
msiInfo Man page
msiInfo,MIAPE-Imaging-method Man page
msiInfo,MSContinuousImagingExperiment-method Man page
msiInfo,MSImageSet-method Man page
msiInfo,MSImagingExperiment-method Man page
msiInfo,MSProcessedImagingExperiment-method Man page
mutate Man page
mutate.DataFrame Source code
mutate.SparseImagingExperiment Man page Source code
mutate.SummaryDataFrame Source code
mutate.XDataFrame Source code
mz Man page
mz,MSImageSet-method Man page
mz,MSImagingExperiment-method Man page
mz,MassDataFrame-method Man page
mz,missing-method Man page
mz-methods Man page
mz<- Man page
mz<-,MSImageSet-method Man page
mz<-,MSImagingExperiment-method Man page
mz<-,MSProcessedImagingExperiment-method Man page
mz<-,MassDataFrame-method Man page
mzAlign Man page
mzAlign,MSImagingExperiment,missing-method Man page
mzAlign,MSImagingExperiment,numeric-method Man page
mzAlign-methods Man page
mzAlign_fun Source code
mzAlign_plotfun Source code
mzAlign_prefun Source code
mzBin Man page
mzBin,MSImagingExperiment,missing-method Man page
mzBin,MSImagingExperiment,numeric-method Man page
mzBin-methods Man page
mzBin_fun Source code
mzBin_plotfun Source code
mzBin_postfun Source code
mzData Man page
mzData,MSImageData-method Man page
mzData,MSImagingInfo-method Man page
mzData,MSProcessedImagingExperiment-method Man page
mzData,SImageData-method Man page
mzData-methods Man page
mzData<- Man page
mzData<-,MSImageData-method Man page
mzData<-,MSProcessedImagingExperiment-method Man page
mzData<-,SImageData-method Man page
mzFilter Man page
mzFilter,MSImagingExperiment-method Man page
mzFilter-methods Man page
mzFilter_postfun Source code
names,ImageData-method Man page
names,ImageList-method Man page
names,ImagingExperiment-method Man page
names,ResultSet-method Man page
names,XDataFrame-method Man page
names<-,ImageData-method Man page
names<-,ImageList-method Man page
names<-,ImagingExperiment-method Man page
nearest_locmax Source code
neg Source code
nipals.OPLS Source code
nipals.PCA Source code
nipals.PLS Source code
nomissing Source code
normalization Man page
normalization,MSImageProcess-method Man page
normalization,Vector-method Man page
normalization<- Man page
normalization<-,MSImageProcess-method Man page
normalization<-,Vector-method Man page
normalize Man page
normalize,MSImageSet-method Man page
normalize,SparseImagingExperiment-method Man page
normalize-methods Man page
normalize.do Source code
normalize.image.linear Source code
normalize.image.method Source code
normalize.method Source code
normalize.method2 Source code
normalize.reference Man page Source code
normalize.rms Man page Source code
normalize.tic Man page Source code
normalize_plotfun Source code
notes,MIAPE-Imaging-method Man page
notes<-,MIAPE-Imaging,character-method Man page
notes<-,MIAPE-Imaging,list-method Man page
otherInfo,MIAPE-Imaging-method Man page
pData Man page
pData,Hashmat-method Man page
pData,ImagingExperiment-method Man page
pData,iSet-method Man page
pData-methods Man page
pData<- Man page
pData<-,Hashmat,ANY-method Man page
pData<-,Hashmat-method Man page
pData<-,ImagingExperiment,ANY-method Man page
pData<-,iSet,ANY-method Man page
pData<-,iSet-method Man page
peakAlign Man page
peakAlign,MSImageSet,MSImageSet-method Man page
peakAlign,MSImageSet,missing-method Man page
peakAlign,MSImageSet,numeric-method Man page
peakAlign,MSImagingExperiment,character-method Man page
peakAlign,MSImagingExperiment,missing-method Man page
peakAlign,MSImagingExperiment,numeric-method Man page
peakAlign-methods Man page
peakAlign.DP Man page Source code
peakAlign.diff Man page Source code
peakAlign.do Source code
peakAlign.method Source code
peakAlign_postfun Source code
peakAlign_prefun Source code
peakBin Man page
peakBin,MSImagingExperiment,missing-method Man page
peakBin,MSImagingExperiment,numeric-method Man page
peakBin-methods Man page
peakBin_fun Source code
peakBin_plotfun Source code
peakBin_postfun Source code
peakBin_prefun Source code
peakData Man page
peakData,MSImageData-method Man page
peakData,MSImagingExperiment-method Man page
peakData,SImageData-method Man page
peakData-methods Man page
peakData<- Man page
peakData<-,MSImageData-method Man page
peakData<-,MSImagingExperiment-method Man page
peakData<-,SImageData-method Man page
peakFilter Man page
peakFilter,MSImageSet-method Man page
peakFilter,MSImagingExperiment-method Man page
peakFilter-methods Man page
peakFilter.freq Man page Source code
peakFilter.method Source code
peakPick Man page
peakPick,MSImageSet-method Man page
peakPick,MSImagingExperiment-method Man page
peakPick-methods Man page
peakPick.adaptive Man page Source code
peakPick.adaptive2 Source code
peakPick.do Source code
peakPick.limpic Man page Source code
peakPick.mad Man page Source code
peakPick.method Source code
peakPick.method2 Source code
peakPick.simple Man page Source code
peakPick.simple2 Source code
peakPick_fun Source code
peakPick_plotfun Source code
peakPick_postfun Source code
peakPicking Man page
peakPicking,MSImageProcess-method Man page
peakPicking,Vector-method Man page
peakPicking<- Man page
peakPicking<-,MSImageProcess-method Man page
peakPicking<-,Vector-method Man page
peaks Man page
peaks,MSImageSet-method Man page
peaks,MSImagingExperiment-method Man page
peaks-methods Man page
peaks<- Man page
peaks<-,MSImageSet-method Man page
peaks<-,MSImagingExperiment-method Man page
phenoData Man page
phenoData,ImagingExperiment-method Man page
phenoData-methods Man page
phenoData<- Man page
phenoData<-,ImagingExperiment,ANY-method Man page
pixelApply Man page
pixelApply,SImageSet-method Man page
pixelApply,SparseImagingExperiment-method Man page
pixelApply-methods Man page
pixelData Man page
pixelData,ImagingExperiment-method Man page
pixelData,SparseImagingExperiment-method Man page
pixelData,iSet-method Man page
pixelData-methods Man page
pixelData<- Man page
pixelData<-,ImagingExperiment-method Man page
pixelData<-,SparseImagingExperiment-method Man page
pixelData<-,iSet-method Man page
pixelNames Man page
pixelNames,IAnnotatedDataFrame-method Man page
pixelNames,ImagingExperiment-method Man page
pixelNames,SImageData-method Man page
pixelNames,SparseImagingExperiment-method Man page
pixelNames,iSet-method Man page
pixelNames-methods Man page
pixelNames<- Man page
pixelNames<-,IAnnotatedDataFrame-method Man page
pixelNames<-,ImagingExperiment-method Man page
pixelNames<-,SImageData-method Man page
pixelNames<-,SImageSet-method Man page
pixelNames<-,SparseImagingExperiment-method Man page
pixelNames<-,iSet-method Man page
pixelSize Man page
pixelSize,MIAPE-Imaging-method Man page
pixelSize,Vector-method Man page
pixels Man page
pixels,MSImageSet-method Man page
pixels,MSImagingExperiment-method Man page
pixels,SparseImagingExperiment-method Man page
pixels,iSet-method Man page
pixels-methods Man page
plasma Man page
plot Man page
plot,AnnotatedImage,ANY-method Man page
plot,AnnotatedImageList,ANY-method Man page
plot,AnnotatedImagingExperiment,ANY-method Man page
plot,CrossValidated,missing-method Man page
plot,DataFrame,ANY-method Man page
plot,MSImageSet,formula-method Man page
plot,MSImageSet,missing-method Man page
plot,MSImagingExperiment,formula-method Man page
plot,MSImagingExperiment,missing-method Man page
plot,MSImagingSummary,missing-method Man page
plot,MassDataFrame,formula-method Man page
plot,MassDataFrame,missing-method Man page
plot,MeansTest,missing-method Man page
plot,OPLS,missing-method Man page
plot,PCA,missing-method Man page
plot,PCA2,missing-method Man page
plot,PLS,missing-method Man page
plot,PLS2,missing-method Man page
plot,ResultSet,formula-method Man page
plot,ResultSet,missing-method Man page
plot,SImageSet,formula-method Man page
plot,SImageSet,missing-method Man page
plot,SegmentationTest,missing-method Man page
plot,SparseImagingExperiment,formula-method Man page
plot,SparseImagingExperiment,missing-method Man page
plot,SparseImagingResult,formula-method Man page
plot,SparseImagingResult,missing-method Man page
plot,SparseImagingSummary,formula-method Man page
plot,SparseImagingSummary,missing-method Man page
plot,SpatialDGMM,missing-method Man page
plot,SpatialFastmap,missing-method Man page
plot,SpatialFastmap2,missing-method Man page
plot,SpatialKMeans,missing-method Man page
plot,SpatialKMeans2,missing-method Man page
plot,SpatialShrunkenCentroids,missing-method Man page
plot,SpatialShrunkenCentroids2,missing-method Man page
plot,XDataFrame,formula-method Man page
plot,XDataFrame,missing-method Man page
plot-methods Man page
plot.summary.CrossValidated Man page Source code
plot.summary.OPLS Man page Source code
plot.summary.PCA Man page Source code
plot.summary.PLS Man page Source code
plot.summary.SpatialFastmap Man page Source code
plot.summary.SpatialKMeans Man page Source code
plot.summary.SpatialShrunkenCentroids Man page Source code
plot_density Source code
points3d Source code
pos Source code
positionArray Man page
positionArray,SImageData-method Man page
positionArray<- Man page
positionArray<-,SImageData-method Man page
predict,OPLS-method Man page
predict,PCA-method Man page Man page
predict,PCA2-method Man page
predict,PLS-method Man page
predict,PLS2-method Man page
predict,SpatialShrunkenCentroids-method Man page
predict,SpatialShrunkenCentroids2-method Man page
preproc,MIAPE-Imaging-method Man page
preproc,SparseImagingExperiment-method Man page
preproc<-,MIAPE-Imaging-method Man page
presetImageDef Man page Source code
print.facet.bar Source code
print.facet.boxplot Source code
print.facet.hist Source code
print.facet.image Source code
print.facet.plot Source code
print.facet.raster Source code
print.summary.CrossValidated Man page Source code
print.summary.OPLS Man page Source code
print.summary.PCA Man page Source code
print.summary.PLS Man page Source code
print.summary.SpatialFastmap Man page Source code
print.summary.SpatialKMeans Man page Source code
print.summary.SpatialShrunkenCentroids Man page Source code
print.summary.iSet Man page Source code
process Man page
process,MSImagingExperiment-method Man page
process,SparseImagingExperiment-method Man page
process-methods Man page
processingData Man page
processingData,MSImageSet-method Man page
processingData,SparseImagingExperiment-method Man page
processingData-methods Man page
processingData<- Man page
processingData<-,MSImageSet-method Man page
processingData<-,SparseImagingExperiment-method Man page
projectToRaster Source code
projectToRaster3d Source code
protocolData,iSet-method Man page
protocolData<-,iSet,ANY-method Man page
pubMedIds,MIAPE-Imaging-method Man page
pubMedIds<-,MIAPE-Imaging,ANY-method Man page
pull,MSImagingExperiment-method Man page
pull,MSProcessedImagingExperiment-method Man page
pull,SparseImagingExperiment-method Man page
range,AnnotatedImage-method Man page
rbind,AnnotatedImageList-method Man page
rbind,Hashmat-method Man page
rbind,ImageArrayList-method Man page
rbind,ImagingExperiment-method Man page
rbind,MSImagingExperiment-method Man page
rbind,MassDataFrame-method Man page
rbind,PositionDataFrame-method Man page
rbind,SparseImagingExperiment-method Man page
rbind,SparseImagingResult-method Man page
rbind,XDataFrame-method Man page
readAnalyze Man page Source code
readImzML Man page Source code
readMSIData Man page Source code
reduceBaseline Man page
reduceBaseline,MSImageSet-method Man page
reduceBaseline,SparseImagingExperiment-method Man page
reduceBaseline-methods Man page
reduceBaseline.do Source code
reduceBaseline.locmin Man page Source code
reduceBaseline.median Man page Source code
reduceBaseline.method Source code
reduceBaseline.method2 Source code
reduceBaseline_plotfun Source code
reduceDimension Man page
reduceDimension,MSImageSet,MSImageSet-method Man page
reduceDimension,MSImageSet,missing-method Man page
reduceDimension,MSImageSet,numeric-method Man page
reduceDimension-methods Man page
reduceDimension.bin Man page Source code
reduceDimension.do Source code
reduceDimension.method Source code
reduceDimension.peaks Man page Source code
reduceDimension.resample Man page Source code
regeneratePositions Man page
regeneratePositions,SImageData-method Man page
regeneratePositions,SImageSet-method Man page
regpr Source code
resolution Man page
resolution,AnnotatedImage-method Man page
resolution,AnnotatedImagingExperiment-method Man page
resolution,MSImagingExperiment-method Man page
resolution,MassDataFrame-method Man page
resolution,PositionDataFrame-method Man page
resolution,SparseImagingExperiment-method Man page
resolution<- Man page
resolution<-,AnnotatedImage-method Man page
resolution<-,MSImagingExperiment-method Man page
resolution<-,MSProcessedImagingExperiment-method Man page
resolution<-,MassDataFrame-method Man page
resolution<-,PositionDataFrame-method Man page
resolution<-,SparseImagingExperiment-method Man page
resultData Man page
resultData,ImagingResult,ANY-method Man page
resultData,ImagingResult,missing-method Man page
resultData,ResultSet,ANY-method Man page
resultData,ResultSet-method Man page
resultData<- Man page
resultData<-,ImagingResult,ANY-method Man page
resultData<-,ImagingResult,missing-method Man page
resultData<-,ResultSet,missing-method Man page
resultData<-,ResultSet-method Man page
resultNames Man page
resultNames,ImagingResult-method Man page
resultNames<- Man page
risk.colors Man page Source code
roundnear Source code
rownames,Hashmat-method Man page
rownames<-,Hashmat-method Man page
run Man page
run,PositionDataFrame-method Man page
run,SparseImagingExperiment-method Man page
run<- Man page
run<-,PositionDataFrame-method Man page
run<-,SparseImagingExperiment-method Man page
runNames Man page
runNames,PositionDataFrame-method Man page
runNames,SparseImagingExperiment-method Man page
runNames<- Man page
runNames<-,PositionDataFrame-method Man page
runNames<-,SparseImagingExperiment-method Man page
sampleNames Man page
sampleNames,IAnnotatedDataFrame-method Man page
sampleNames,ImagingExperiment-method Man page
sampleNames,iSet-method Man page
sampleNames-methods Man page
sampleNames<- Man page
sampleNames<-,IAnnotatedDataFrame,ANY-method Man page
sampleNames<-,IAnnotatedDataFrame-method Man page
sampleNames<-,ImagingExperiment,ANY-method Man page
sampleNames<-,iSet,ANY-method Man page
sampleNames<-,iSet-method Man page
samples,MIAPE-Imaging-method Man page
scanDirection Man page
scanDirection,MIAPE-Imaging-method Man page
scanDirection,Vector-method Man page
scanPattern Man page
scanPattern,MIAPE-Imaging-method Man page
scanPattern,Vector-method Man page
scanPolarity Man page
scanPolarity,MIAPE-Imaging-method Man page
scanPolarity,Vector-method Man page
scanType Man page
scanType,MIAPE-Imaging-method Man page
scanType,Vector-method Man page
scans,MSImagingInfo-method Man page
segmentationTest Man page
segmentationTest,SparseImagingExperiment-method Man page
segmentationTest,SpatialDGMM-method Man page
segmentationTest-methods Man page
select Man page
select.DataFrame Source code
select.SparseImagingExperiment Man page Source code
select.SummaryDataFrame Source code
select.XDataFrame Source code
selectROI Man page
selectROI,SImageSet-method Man page
selectROI,SparseImagingExperiment-method Man page
selectROI-methods Man page
sensitivity Source code
seq.ppm Source code
setCardinalBPPARAM Man page Source code
setCardinalDelayProc Man page Source code
setCardinalNumBlocks Man page Source code
setCardinalVerbose Man page Source code
setRNGStream Source code
setup.layout Man page Source code
show,AnnotatedImageList-method Man page
show,AnnotatedImagingExperiment-method Man page
show,Hashmat-method Man page
show,IAnnotatedDataFrame-method Man page
show,ImageData-method Man page
show,ImagingExperiment-method Man page
show,ImagingResult-method Man page
show,MIAPE-Imaging-method Man page
show,MSImageProcess-method Man page
show,MSImageSet-method Man page
show,MSImagingExperiment-method Man page
show,ResultSet-method Man page
show,SimpleImageList-method Man page
show,SparseImagingExperiment-method Man page
show,SparseImagingResult-method Man page
show,SummaryDataFrame-method Man page
show,XDataFrame-method Man page
show,iSet-method Man page
showNames Man page
showNames,MassDataFrame-method Man page
showNames,PositionDataFrame-method Man page
showNames,XDataFrame-method Man page
simulateImage Man page Source code
simulateSpectrum Man page Source code
slice Man page
slice,SparseImagingExperiment-method Man page
slice.SparseImagingExperiment Man page Source code
smooth Man page
smooth,SparseImagingExperiment-method Man page
smooth-methods Man page
smooth.image.adaptive Source code
smooth.image.gaussian Source code
smooth.image.method Source code
smoothSignal Man page
smoothSignal,MSImageSet-method Man page
smoothSignal,SparseImagingExperiment-method Man page
smoothSignal-methods Man page
smoothSignal.do Source code
smoothSignal.gaussian Man page Source code
smoothSignal.kaiser Source code
smoothSignal.ma Man page Source code
smoothSignal.method Source code
smoothSignal.method2 Source code
smoothSignal.sgolay Man page Source code
smoothSignal_plotfun Source code
smoothing Man page
smoothing,MSImageProcess-method Man page
smoothing,Vector-method Man page
smoothing<- Man page
smoothing<-,MSImageProcess-method Man page
smoothing<-,Vector-method Man page
soft Source code
softwareName Man page
softwareName,MIAPE-Imaging-method Man page
softwareVersion Man page
softwareVersion,MIAPE-Imaging-method Man page
sort,XDataFrame-method Man page
spatialApply Man page
spatialApply,SparseImagingExperiment-method Man page
spatialApply-methods Man page
spatialDGMM Man page
spatialDGMM,SparseImagingExperiment-method Man page
spatialDGMM-methods Man page
spatialFastmap Man page
spatialFastmap,SImageSet-method Man page
spatialFastmap,SparseImagingExperiment-method Man page
spatialFastmap-class Man page
spatialFastmap-methods Man page
spatialKMeans Man page
spatialKMeans,SImageSet-method Man page
spatialKMeans,SparseImagingExperiment-method Man page
spatialKMeans-methods Man page
spatialShrunkenCentroids Man page
spatialShrunkenCentroids,SImageSet,character-method Man page
spatialShrunkenCentroids,SImageSet,factor-method Man page
spatialShrunkenCentroids,SImageSet,missing-method Man page
spatialShrunkenCentroids,SparseImagingExperiment,ANY-method Man page
spatialShrunkenCentroids,SparseImagingExperiment,missing-method Man page
spatialShrunkenCentroids-methods Man page
spatialWeights Man page
spatialWeights,IAnnotatedDataFrame-method Man page
spatialWeights,ImagingExperiment-method Man page
spatialWeights,PositionDataFrame-method Man page
spatialWeights,iSet-method Man page
spatialWeights-methods Man page
specificity Source code
specimenOrigin Man page
specimenOrigin,MIAPE-Imaging-method Man page
specimenType Man page
specimenType,MIAPE-Imaging-method Man page
spectra Man page
spectra,MSImageSet-method Man page
spectra,MSImagingExperiment-method Man page
spectra-methods Man page
spectra<- Man page
spectra<-,MSImageSet-method Man page
spectra<-,MSImagingExperiment-method Man page
spectraData Man page
spectraData,MSImagingExperiment-method Man page
spectraData-methods Man page
spectraData<- Man page
spectraData<-,MSImagingExperiment-method Man page
spectrumRepresentation Man page
spectrumRepresentation,MSImageProcess-method Man page
spectrumRepresentation,Vector-method Man page
spectrumRepresentation<- Man page
spectrumRepresentation<-,MSImageProcess-method Man page
spectrumRepresentation<-,Vector-method Man page
split_blocks Source code
stainingMethod Man page
stainingMethod,MIAPE-Imaging-method Man page
standardizeRuns Man page
standardizeRuns,MSImageSet-method Man page
standardizeRuns-methods Man page
standardizeRuns.method Source code
standardizeRuns.sum Man page Source code
storageMode,ImageData-method Man page
storageMode,iSet-method Man page
storageMode<-,ImageData,character-method Man page
storageMode<-,iSet,ANY-method Man page
storageMode<-,iSet,character-method Man page
subset,SparseImagingExperiment-method Man page
subsetFeatures Man page Source code
subsetPixels Man page Source code
subset_data Source code
subset_rows Source code
summarise Man page
summarise.DataFrame Source code
summarise.MSImagingExperiment Man page Source code
summarise.SparseImagingExperiment Man page Source code
summarise.SummaryDataFrame Source code
summarise.XDataFrame Source code
summarize Man page
summarizeFeatures Man page Source code
summarizePixels Man page Source code
summary,CrossValidated-method Man page
summary,CrossValidated2-method Man page
summary,MeansTest-method Man page
summary,OPLS-method Man page
summary,PCA-method Man page
summary,PCA2-method Man page
summary,PLS-method Man page
summary,PLS2-method Man page
summary,SegmentationTest-method Man page
summary,SpatialDGMM-method Man page
summary,SpatialFastmap-method Man page
summary,SpatialFastmap2-method Man page
summary,SpatialKMeans-method Man page
summary,SpatialKMeans2-method Man page
summary,SpatialShrunkenCentroids-method Man page
summary,SpatialShrunkenCentroids2-method Man page
summary,SummaryDataFrame-method Man page
summary,iSet-method Man page
tissueThickness Man page
tissueThickness,MIAPE-Imaging-method Man page
tissueWash Man page
tissueWash,MIAPE-Imaging-method Man page
tolerance,MSProcessedImagingExperiment-method Man page
tolerance,MSProcessedImagingSpectraList-method Man page
tolerance<-,MSProcessedImagingExperiment-method Man page
tolerance<-,MSProcessedImagingSpectraList-method Man page
topFeatures Man page
topFeatures,CrossValidated-method Man page
topFeatures,MeansTest-method Man page
topFeatures,OPLS-method Man page
topFeatures,PCA-method Man page
topFeatures,PLS-method Man page
topFeatures,ResultSet-method Man page
topFeatures,SegmentationTest-method Man page
topFeatures,SpatialKMeans-method Man page
topFeatures,SpatialKMeans2-method Man page
topFeatures,SpatialShrunkenCentroids-method Man page
topFeatures,SpatialShrunkenCentroids2-method Man page
topFeatures-methods Man page
ungroup Man page
ungroup.XDataFrame Source code
varLabels,iSet-method Man page
varLabels<-,iSet-method Man page
varMetadata,iSet-method Man page
varMetadata<-,iSet,ANY-method Man page
varMetadata<-,iSet-method Man page
viridis Man page
width,AnnotatedImage-method Man page
width,AnnotatedImagingExperiment-method Man page
width<-,AnnotatedImage-method Man page
wrap Source code
writeAnalyze Man page Source code
writeAnalyze,MSImageSet-method Man page
writeImzML Man page Source code
writeImzML,MSImageSet-method Man page
writeMSIData Man page Source code
writeMSIData,MSImageSet,character-method Man page
Cardinal documentation built on Nov. 8, 2020, 11:10 p.m.

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