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 |
| abstract-method | Legacy classes and methods in Cardinal |
| addShape | Simulate a mass spectrum or MS imaging experiment |
| aggregate-method | Calculating summary statistics |
| alpha.colors | Color palettes for imaging |
| annotatedDataFrameFrom-method | Legacy classes and methods in Cardinal |
| AnnotatedImage | AnnotatedImage: Optical images with annotations |
| AnnotatedImage-class | AnnotatedImage: Optical images with annotations |
| AnnotatedImageList | AnnotatedImagingExperiment: Mass spectrometry imaging experiments |
| AnnotatedImageList-class | AnnotatedImagingExperiment: Mass spectrometry imaging experiments |
| AnnotatedImagingExperiment | AnnotatedImagingExperiment: Mass spectrometry imaging experiments |
| AnnotatedImagingExperiment-class | AnnotatedImagingExperiment: Mass spectrometry imaging experiments |
| arrange | Deprecated functions and methods in Cardinal |
| as.data.frame-method | XDataFrame: DataFrame with eXtra metadata columns |
| as.env-method | XDataFrame: DataFrame with eXtra metadata columns |
| as.list-method | ImageList: Abstract image data list |
| as.list-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| as.list-method | MassDataFrame: data frame with mass-to-charge ratio metadata |
| as.list-method | PositionDataFrame: data frame with spatial position metadata |
| as.matrix-method | XDataFrame: DataFrame with eXtra metadata columns |
| baselineReduction | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| baselineReduction-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| baselineReduction-method | Legacy classes and methods in Cardinal |
| baselineReduction<- | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| baselineReduction<--method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| baselineReduction<--method | Legacy classes and methods in Cardinal |
| batchProcess | Legacy classes and methods in Cardinal |
| batchProcess-method | Legacy classes and methods in Cardinal |
| batchProcess-methods | Legacy classes and methods in Cardinal |
| bw.colors | Color palettes for imaging |
| Cardinal | Mass spectrometry imaging tools |
| Cardinal-legacy | Legacy classes and methods in Cardinal |
| Cardinal-reexports | Objects exported from other packages |
| CardinalLog | Mass spectrometry imaging tools |
| CardinalVersion | Mass spectrometry imaging tools |
| cbind-method | AnnotatedImagingExperiment: Mass spectrometry imaging experiments |
| cbind-method | ImageList: Abstract image data list |
| cbind-method | ImagingExperiment: Abstract class for imaging experiments |
| cbind-method | ImagingResult: Results of statistical analysis of imaging experiments |
| cbind-method | MSImagingExperiment: Mass spectrometry imaging experiments |
| cbind-method | MassDataFrame: data frame with mass-to-charge ratio metadata |
| cbind-method | PositionDataFrame: data frame with spatial position metadata |
| cbind-method | SparseImagingExperiment: Pixel-sparse imaging experiments |
| cbind-method | XDataFrame: DataFrame with eXtra metadata columns |
| cbind-method | Legacy classes and methods in Cardinal |
| centroided | MSImagingExperiment: Mass spectrometry imaging experiments |
| centroided-method | MSImagingExperiment: Mass spectrometry imaging experiments |
| centroided-method | Legacy classes and methods in Cardinal |
| centroided<- | MSImagingExperiment: Mass spectrometry imaging experiments |
| centroided<--method | MSImagingExperiment: Mass spectrometry imaging experiments |
| centroided<--method | Legacy classes and methods in Cardinal |
| cividis | Objects exported from other packages |
| class:AnnotatedImage | AnnotatedImage: Optical images with annotations |
| class:AnnotatedImageList | AnnotatedImagingExperiment: Mass spectrometry imaging experiments |
| class:AnnotatedImagingExperiment | AnnotatedImagingExperiment: Mass spectrometry imaging experiments |
| class:Hashmat | Legacy classes and methods in Cardinal |
| class:IAnnotatedDataFrame | Legacy classes and methods in Cardinal |
| class:ImageArrayList | ImageList: Abstract image data list |
| class:ImageData | Legacy classes and methods in Cardinal |
| class:ImageList | ImageList: Abstract image data list |
| class:ImagingExperiment | ImagingExperiment: Abstract class for imaging experiments |
| class:ImagingResult | ImagingResult: Results of statistical analysis of imaging experiments |
| class:iSet | Legacy classes and methods in Cardinal |
| class:MassDataFrame | MassDataFrame: data frame with mass-to-charge ratio metadata |
| class:MeansTest | Linear model-based testing for summarized imaging experiments |
| class:MIAPE-Imaging | Legacy classes and methods in Cardinal |
| class:MSContinuousImagingExperiment | MSContinuousImagingExperiment: "Continuous" mass spectrometry imaging experiments |
| class:MSContinuousImagingSpectraList | ImageList: Abstract image data list |
| class:MSImageData | Legacy classes and methods in Cardinal |
| class:MSImageProcess | Legacy classes and methods in Cardinal |
| class:MSImageSet | Legacy classes and methods in Cardinal |
| class:MSImagingExperiment | MSImagingExperiment: Mass spectrometry imaging experiments |
| class:MSImagingInfo | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| class:MSProcessedImagingExperiment | MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments |
| class:MSProcessedImagingSpectraList | ImageList: Abstract image data list |
| class:OPLS | Partial least squares |
| class:PCA | Principal components analysis |
| class:PLS | Partial least squares |
| class:PositionDataFrame | PositionDataFrame: data frame with spatial position metadata |
| class:ResultSet | Legacy classes and methods in Cardinal |
| class:SegmentationTest | Linear model-based testing for summarized imaging experiments |
| class:SImageData | Legacy classes and methods in Cardinal |
| class:SImageSet | Legacy classes and methods in Cardinal |
| class:SimpleImageArrayList | ImageList: Abstract image data list |
| class:SimpleImageList | ImageList: Abstract image data list |
| class:SparseImagingExperiment | SparseImagingExperiment: Pixel-sparse imaging experiments |
| class:SparseImagingResult | ImagingResult: Results of statistical analysis of imaging experiments |
| class:SpatialDGMM | Spatially-aware Dirichlet Gaussian mixture model |
| class:spatialFastmap | Spatially-aware FastMap projection |
| class:SpatialKMeans | Spatially-aware k-means clustering |
| class:SpatialShrunkenCentroids | Spatially-aware shrunken centroid clustering and classification |
| class:XDataFrame | XDataFrame: DataFrame with eXtra metadata columns |
| col.map | Color palettes for imaging |
| collect | Deprecated functions and methods in Cardinal |
| collect.MSImagingExperiment | Deprecated functions and methods in Cardinal |
| collect.MSProcessedImagingExperiment | Deprecated functions and methods in Cardinal |
| collect.SparseImagingExperiment | Deprecated functions and methods in Cardinal |
| colnames-method | Legacy classes and methods in Cardinal |
| colnames<--method | Legacy classes and methods in Cardinal |
| colocalized | Colocalized features |
| colocalized-method | Colocalized features |
| color.map | Color palettes for imaging |
| combine-method | AnnotatedImagingExperiment: Mass spectrometry imaging experiments |
| combine-method | ImagingExperiment: Abstract class for imaging experiments |
| combine-method | ImagingResult: Results of statistical analysis of imaging experiments |
| combine-method | SparseImagingExperiment: Pixel-sparse imaging experiments |
| combine-method | Legacy classes and methods in Cardinal |
| combiner-method | MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments |
| combiner<--method | MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments |
| coord | PositionDataFrame: data frame with spatial position metadata |
| coord-method | AnnotatedImage: Optical images with annotations |
| coord-method | AnnotatedImagingExperiment: Mass spectrometry imaging experiments |
| coord-method | PositionDataFrame: data frame with spatial position metadata |
| coord-method | SparseImagingExperiment: Pixel-sparse imaging experiments |
| coord-method | Legacy classes and methods in Cardinal |
| coord-methods | PositionDataFrame: data frame with spatial position metadata |
| coord<- | PositionDataFrame: data frame with spatial position metadata |
| coord<--method | AnnotatedImage: Optical images with annotations |
| coord<--method | PositionDataFrame: data frame with spatial position metadata |
| coord<--method | SparseImagingExperiment: Pixel-sparse imaging experiments |
| coord<--method | Legacy classes and methods in Cardinal |
| coordinates | PositionDataFrame: data frame with spatial position metadata |
| coordinates-method | AnnotatedImage: Optical images with annotations |
| coordinates-method | AnnotatedImagingExperiment: Mass spectrometry imaging experiments |
| 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 | AnnotatedImage: Optical images with annotations |
| 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 | PositionDataFrame: data frame with spatial position metadata |
| coordLabels-method | SparseImagingExperiment: Pixel-sparse imaging experiments |
| coordLabels-method | Legacy classes and methods in Cardinal |
| coordLabels-methods | PositionDataFrame: data frame with spatial position metadata |
| coordLabels<- | PositionDataFrame: data frame with spatial position metadata |
| coordLabels<--method | PositionDataFrame: data frame with spatial position metadata |
| coordLabels<--method | SparseImagingExperiment: Pixel-sparse imaging experiments |
| coordLabels<--method | Legacy classes and methods in Cardinal |
| coordnames | PositionDataFrame: data frame with spatial position metadata |
| coordnames-method | PositionDataFrame: data frame with spatial position metadata |
| coordnames-method | SparseImagingExperiment: Pixel-sparse imaging experiments |
| coordnames-methods | PositionDataFrame: data frame with spatial position metadata |
| coordnames<- | PositionDataFrame: data frame with spatial position metadata |
| coordnames<--method | PositionDataFrame: data frame with spatial position metadata |
| coordnames<--method | SparseImagingExperiment: Pixel-sparse imaging experiments |
| crossValidate | Apply cross-validation to imaging analyses |
| crossValidate-method | Apply cross-validation to imaging analyses |
| crossValidate-methods | Apply cross-validation to imaging analyses |
| cvApply | Apply cross-validation to imaging analyses |
| cvApply-method | Apply cross-validation to imaging analyses |
| cvApply-methods | Apply cross-validation to imaging analyses |
| darkmode | Color palettes for imaging |
| Defunct | Defunct functions and methods in Cardinal |
| Deprecated | Deprecated functions and methods in Cardinal |
| dim-method | AnnotatedImagingExperiment: Mass spectrometry imaging experiments |
| dim-method | ImageList: Abstract image data list |
| dim-method | ImagingExperiment: Abstract class for imaging experiments |
| dim-method | SparseImagingExperiment: Pixel-sparse imaging experiments |
| dim-method | Legacy classes and methods in Cardinal |
| dim<--method | Legacy classes and methods in Cardinal |
| dimnames-method | ImagingExperiment: Abstract class for imaging experiments |
| dimnames-method | Legacy classes and methods in Cardinal |
| dimnames<--method | Legacy classes and methods in Cardinal |
| dims-method | AnnotatedImagingExperiment: Mass spectrometry imaging experiments |
| dims-method | ImageList: Abstract image data list |
| dims-method | PositionDataFrame: data frame with spatial position metadata |
| dims-method | SparseImagingExperiment: Pixel-sparse imaging experiments |
| dims-method | Legacy classes and methods in Cardinal |
| discrete.colors | Color palettes for imaging |
| divergent.colors | Color palettes for imaging |
| embeddingMethod | Legacy classes and methods in Cardinal |
| embeddingMethod-method | Legacy classes and methods in Cardinal |
| experimentData-method | Legacy classes and methods in Cardinal |
| experimentData<--method | Legacy classes and methods in Cardinal |
| expinfo-method | Legacy classes and methods in Cardinal |
| fData | ImagingExperiment: Abstract class for imaging experiments |
| fData-method | ImagingExperiment: Abstract class for imaging experiments |
| fData-method | Legacy classes and methods in Cardinal |
| 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 | Legacy classes and methods in Cardinal |
| 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 | Legacy classes and methods in Cardinal |
| 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 | Legacy classes and methods in Cardinal |
| featureNames | ImagingExperiment: Abstract class for imaging experiments |
| featureNames-method | ImagingExperiment: Abstract class for imaging experiments |
| featureNames-method | Legacy classes and methods in Cardinal |
| 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 | Legacy classes and methods in Cardinal |
| features | SparseImagingExperiment: Pixel-sparse imaging experiments |
| features-method | MSImagingExperiment: Mass spectrometry imaging experiments |
| features-method | SparseImagingExperiment: Pixel-sparse imaging experiments |
| features-method | Legacy classes and methods in Cardinal |
| features-methods | SparseImagingExperiment: Pixel-sparse imaging experiments |
| filter | Deprecated functions and methods in Cardinal |
| filter.SparseImagingExperiment | Deprecated functions and methods in Cardinal |
| 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 | Legacy classes and methods in Cardinal |
| fvarLabels<--method | Legacy classes and methods in Cardinal |
| fvarMetadata-method | Legacy classes and methods in Cardinal |
| fvarMetadata<--method | Legacy classes and methods in Cardinal |
| generateImage | Defunct functions and methods in Cardinal |
| generateSpectrum | Defunct functions and methods in Cardinal |
| getCardinalBPPARAM | Mass spectrometry imaging tools |
| getCardinalDelayProc | Mass spectrometry imaging tools |
| getCardinalNumBlocks | Mass spectrometry imaging tools |
| getCardinalVerbose | Mass spectrometry imaging tools |
| gradient.colors | Color palettes for imaging |
| gridded-method | PositionDataFrame: data frame with spatial position metadata |
| gridded-method | SparseImagingExperiment: Pixel-sparse imaging experiments |
| gridded<--method | PositionDataFrame: data frame with spatial position metadata |
| gridded<--method | SparseImagingExperiment: Pixel-sparse imaging experiments |
| groups | Deprecated functions and methods in Cardinal |
| group_by | Deprecated functions and methods in Cardinal |
| Hashmat | Legacy classes and methods in Cardinal |
| Hashmat-class | Legacy classes and methods in Cardinal |
| height | AnnotatedImage: Optical images with annotations |
| height-method | AnnotatedImage: Optical images with annotations |
| height-method | AnnotatedImagingExperiment: Mass spectrometry imaging experiments |
| height<- | AnnotatedImage: Optical images with annotations |
| height<--method | AnnotatedImage: Optical images with annotations |
| IAnnotatedDataFrame | Legacy classes and methods in Cardinal |
| IAnnotatedDataFrame-class | Legacy classes and methods in Cardinal |
| iData | ImagingExperiment: Abstract class for imaging experiments |
| iData-method | ImagingExperiment: Abstract class for imaging experiments |
| iData-method | Legacy classes and methods in Cardinal |
| iData-methods | ImagingExperiment: Abstract class for imaging experiments |
| iData<- | ImagingExperiment: Abstract class for imaging experiments |
| iData<--method | ImagingExperiment: Abstract class for imaging experiments |
| iData<--method | MSContinuousImagingExperiment: "Continuous" mass spectrometry imaging experiments |
| iData<--method | MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments |
| iData<--method | Legacy classes and methods in Cardinal |
| 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 | Legacy classes and methods in Cardinal |
| imageData | ImagingExperiment: Abstract class for imaging experiments |
| ImageData-class | Legacy classes and methods in Cardinal |
| imageData-method | ImagingExperiment: Abstract class for imaging experiments |
| imageData-method | Legacy classes and methods in Cardinal |
| imageData-methods | ImagingExperiment: Abstract class for imaging experiments |
| imageData<- | ImagingExperiment: Abstract class for imaging experiments |
| imageData<--method | ImagingExperiment: Abstract class for imaging experiments |
| imageData<--method | MSContinuousImagingExperiment: "Continuous" mass spectrometry imaging experiments |
| imageData<--method | MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments |
| imageData<--method | Legacy classes and methods in Cardinal |
| ImageList | ImageList: Abstract image data list |
| ImageList-class | ImageList: Abstract image data list |
| imageShape | Legacy classes and methods in Cardinal |
| imageShape-method | Legacy classes and methods in Cardinal |
| ImagingExperiment | ImagingExperiment: Abstract class for imaging experiments |
| ImagingExperiment-class | ImagingExperiment: Abstract class for imaging experiments |
| ImagingResult | ImagingResult: Results of statistical analysis of imaging experiments |
| ImagingResult-class | ImagingResult: Results of statistical analysis of imaging experiments |
| inferno | Objects exported from other packages |
| initialize-method | MassDataFrame: data frame with mass-to-charge ratio metadata |
| initialize-method | PositionDataFrame: data frame with spatial position metadata |
| initialize-method | Legacy classes and methods in Cardinal |
| inSituChemistry | Legacy classes and methods in Cardinal |
| inSituChemistry-method | Legacy classes and methods in Cardinal |
| instrumentModel | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| instrumentModel-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| instrumentModel-method | Legacy classes and methods in Cardinal |
| instrumentVendor | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| instrumentVendor-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| instrumentVendor-method | Legacy classes and methods in Cardinal |
| intensity.colors | Color palettes for imaging |
| intensityData | MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments |
| intensityData-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| intensityData-method | MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments |
| intensityData-methods | MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments |
| intensityData<- | MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments |
| intensityData<--method | MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments |
| ionizationType | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| ionizationType-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| ionizationType-method | Legacy classes and methods in Cardinal |
| is3D | SparseImagingExperiment: Pixel-sparse imaging experiments |
| is3D-method | PositionDataFrame: data frame with spatial position metadata |
| is3D-method | SparseImagingExperiment: Pixel-sparse imaging experiments |
| is3D-method | Legacy classes and methods in Cardinal |
| isCentroided | MSImagingExperiment: Mass spectrometry imaging experiments |
| isCentroided-method | MSImagingExperiment: Mass spectrometry imaging experiments |
| isCentroided-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| isCentroided-method | MassDataFrame: data frame with mass-to-charge ratio metadata |
| iSet | Legacy classes and methods in Cardinal |
| iSet-class | Legacy classes and methods in Cardinal |
| jet.colors | Color palettes for imaging |
| keys | Legacy classes and methods in Cardinal |
| keys-method | MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments |
| keys-method | Legacy classes and methods in Cardinal |
| keys<- | Legacy classes and methods in Cardinal |
| keys<--method | MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments |
| keys<--method | Legacy classes and methods in Cardinal |
| lapply-method | XDataFrame: DataFrame with eXtra metadata columns |
| length-method | AnnotatedImage: Optical images with annotations |
| length-method | ImageList: Abstract image data list |
| length-method | ImagingExperiment: Abstract class for imaging experiments |
| length-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| length-method | XDataFrame: DataFrame with eXtra metadata columns |
| length-method | Legacy classes and methods in Cardinal |
| lightmode | Color palettes for imaging |
| lineScanDirection | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| lineScanDirection-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| lineScanDirection-method | Legacy classes and methods in Cardinal |
| logLik-method | Spatially-aware shrunken centroid clustering and classification |
| magma | Objects exported from other packages |
| makeFactor | Select regions-of-interest of an imaging dataset |
| massAnalyzerType | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| massAnalyzerType-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| massAnalyzerType-method | Legacy classes and methods in Cardinal |
| MassDataFrame | MassDataFrame: data frame with mass-to-charge ratio metadata |
| MassDataFrame-class | MassDataFrame: data frame with mass-to-charge ratio metadata |
| matrixApplication | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| matrixApplication-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| matrixApplication-method | Legacy classes and methods in Cardinal |
| meansTest | Linear model-based testing for summarized imaging experiments |
| MeansTest-class | Linear model-based testing for summarized imaging experiments |
| meansTest-method | Linear model-based testing for summarized imaging experiments |
| meansTest-methods | Linear model-based testing for summarized imaging experiments |
| MIAPE-Imaging | Legacy classes and methods in Cardinal |
| MIAPE-Imaging-class | Legacy classes and methods in Cardinal |
| modelData | ImagingResult: Results of statistical analysis of imaging experiments |
| modelData-method | ImagingResult: Results of statistical analysis of imaging experiments |
| modelData-method | Legacy classes and methods in Cardinal |
| modelData<- | ImagingResult: Results of statistical analysis of imaging experiments |
| modelData<--method | ImagingResult: Results of statistical analysis of imaging experiments |
| modelData<--method | Legacy classes and methods in Cardinal |
| MSContinuousImagingExperiment | MSContinuousImagingExperiment: "Continuous" mass spectrometry imaging experiments |
| MSContinuousImagingExperiment-class | MSContinuousImagingExperiment: "Continuous" mass spectrometry imaging experiments |
| MSContinuousImagingSpectraList | ImageList: Abstract image data list |
| MSContinuousImagingSpectraList-class | ImageList: Abstract image data list |
| msiInfo | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| msiInfo-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| msiInfo-method | Legacy classes and methods in Cardinal |
| MSImageData | Legacy classes and methods in Cardinal |
| MSImageData-class | Legacy classes and methods in Cardinal |
| MSImageProcess | Legacy classes and methods in Cardinal |
| MSImageProcess-class | Legacy classes and methods in Cardinal |
| MSImageSet | Legacy classes and methods in Cardinal |
| MSImageSet-class | Legacy classes and methods in Cardinal |
| MSImagingExperiment | MSImagingExperiment: Mass spectrometry imaging experiments |
| MSImagingExperiment-class | MSImagingExperiment: Mass spectrometry imaging experiments |
| MSImagingInfo | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| MSImagingInfo-class | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| MSProcessedImagingExperiment | MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments |
| MSProcessedImagingExperiment-class | MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments |
| MSProcessedImagingSpectraList | ImageList: Abstract image data list |
| MSProcessedImagingSpectraList-class | ImageList: Abstract image data list |
| mutate | Deprecated functions and methods in Cardinal |
| mutate.SparseImagingExperiment | Deprecated functions and methods in Cardinal |
| mz | Manipulate mass-to-charge-ratio values |
| mz-method | MSImagingExperiment: Mass spectrometry imaging experiments |
| mz-method | MassDataFrame: data frame with mass-to-charge ratio metadata |
| mz-method | Legacy classes and methods in Cardinal |
| mz-method | Manipulate mass-to-charge-ratio values |
| mz-methods | Manipulate mass-to-charge-ratio values |
| mz<- | Manipulate mass-to-charge-ratio values |
| mz<--method | MSImagingExperiment: Mass spectrometry imaging experiments |
| mz<--method | MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments |
| mz<--method | MassDataFrame: data frame with mass-to-charge ratio metadata |
| mz<--method | Legacy classes and methods in Cardinal |
| mzAlign | Mass align an imaging dataset |
| mzAlign-method | Mass align an imaging dataset |
| mzAlign-methods | Mass align an imaging dataset |
| mzBin | Mass bin an imaging dataset |
| mzBin-method | Mass bin an imaging dataset |
| mzBin-methods | Mass bin an imaging dataset |
| mzData | MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments |
| mzData-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| mzData-method | MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments |
| mzData-method | Legacy classes and methods in Cardinal |
| mzData-methods | MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments |
| mzData<- | MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments |
| mzData<--method | MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments |
| mzData<--method | Legacy classes and methods in Cardinal |
| mzFilter | Filter the features of an imaging dataset by intensity |
| mzFilter-method | Filter the features of an imaging dataset by intensity |
| mzFilter-methods | Filter the features of an imaging dataset by intensity |
| names-method | ImageList: Abstract image data list |
| names-method | ImagingExperiment: Abstract class for imaging experiments |
| names-method | XDataFrame: DataFrame with eXtra metadata columns |
| names-method | Legacy classes and methods in Cardinal |
| names<--method | ImageList: Abstract image data list |
| names<--method | ImagingExperiment: Abstract class for imaging experiments |
| names<--method | Legacy classes and methods in Cardinal |
| normalization | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| normalization-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| normalization-method | Legacy classes and methods in Cardinal |
| normalization<- | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| normalization<--method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| normalization<--method | Legacy classes and methods in Cardinal |
| 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 | Legacy classes and methods in Cardinal |
| notes<--method | Legacy classes and methods in Cardinal |
| OPLS | Partial least squares |
| OPLS-class | Partial least squares |
| OPLS-method | Partial least squares |
| OPLS-methods | Partial least squares |
| otherInfo-method | Legacy classes and methods in Cardinal |
| PCA | Principal components analysis |
| PCA-class | Principal components analysis |
| PCA-method | Principal components analysis |
| PCA-methods | Principal components analysis |
| pData | ImagingExperiment: Abstract class for imaging experiments |
| pData-method | ImagingExperiment: Abstract class for imaging experiments |
| pData-method | Legacy classes and methods in Cardinal |
| pData-methods | ImagingExperiment: Abstract class for imaging experiments |
| pData<- | ImagingExperiment: Abstract class for imaging experiments |
| pData<--method | ImagingExperiment: Abstract class for imaging experiments |
| pData<--method | Legacy classes and methods in Cardinal |
| peakAlign | Peak align an imaging dataset |
| peakAlign-method | Peak align an imaging dataset |
| peakAlign-methods | Peak align an imaging dataset |
| peakAlign.diff | Peak align an imaging dataset |
| peakAlign.DP | Peak align an imaging dataset |
| peakBin | Peak bin an imaging dataset |
| peakBin-method | Peak bin an imaging dataset |
| peakBin-methods | Peak bin an imaging dataset |
| peakData | MSImagingExperiment: Mass spectrometry imaging experiments |
| peakData-method | MSImagingExperiment: Mass spectrometry imaging experiments |
| peakData-method | Legacy classes and methods in Cardinal |
| peakData-methods | MSImagingExperiment: Mass spectrometry imaging experiments |
| peakData<- | MSImagingExperiment: Mass spectrometry imaging experiments |
| peakData<--method | MSImagingExperiment: Mass spectrometry imaging experiments |
| peakData<--method | Legacy classes and methods in Cardinal |
| peakFilter | Filter the features of an imaging dataset by intensity |
| peakFilter-method | Filter the features of an imaging dataset by intensity |
| peakFilter-methods | Filter the features of an imaging dataset by intensity |
| peakFilter.freq | Filter the features of an imaging dataset by intensity |
| peakPick | Peak pick an imaging dataset |
| peakPick-method | Peak pick an imaging dataset |
| peakPick-methods | Peak pick an imaging dataset |
| peakPick.adaptive | Peak pick an imaging dataset |
| peakPick.limpic | Peak pick an imaging dataset |
| peakPick.mad | Peak pick an imaging dataset |
| peakPick.simple | Peak pick an imaging dataset |
| peakPicking | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| peakPicking-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| peakPicking-method | Legacy classes and methods in Cardinal |
| peakPicking<- | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| peakPicking<--method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| peakPicking<--method | Legacy classes and methods in Cardinal |
| peaks | MSImagingExperiment: Mass spectrometry imaging experiments |
| peaks-method | MSImagingExperiment: Mass spectrometry imaging experiments |
| peaks-method | Legacy classes and methods in Cardinal |
| peaks-methods | MSImagingExperiment: Mass spectrometry imaging experiments |
| peaks<- | MSImagingExperiment: Mass spectrometry imaging experiments |
| peaks<--method | MSImagingExperiment: Mass spectrometry imaging experiments |
| peaks<--method | Legacy classes and methods in Cardinal |
| phenoData | ImagingExperiment: Abstract class for imaging experiments |
| phenoData-method | ImagingExperiment: Abstract class for imaging experiments |
| phenoData-methods | ImagingExperiment: Abstract class for imaging experiments |
| phenoData<- | ImagingExperiment: Abstract class for imaging experiments |
| phenoData<--method | ImagingExperiment: Abstract class for imaging experiments |
| pixelApply | Apply functions over imaging datasets |
| pixelApply-method | Apply functions over imaging datasets |
| pixelApply-methods | Apply functions over imaging datasets |
| pixelData | ImagingExperiment: Abstract class for imaging experiments |
| pixelData-method | ImagingExperiment: Abstract class for imaging experiments |
| pixelData-method | SparseImagingExperiment: Pixel-sparse imaging experiments |
| pixelData-method | Legacy classes and methods in Cardinal |
| pixelData-methods | ImagingExperiment: Abstract class for imaging experiments |
| pixelData<- | ImagingExperiment: Abstract class for imaging experiments |
| pixelData<--method | ImagingExperiment: Abstract class for imaging experiments |
| pixelData<--method | SparseImagingExperiment: Pixel-sparse imaging experiments |
| pixelData<--method | Legacy classes and methods in Cardinal |
| pixelNames | ImagingExperiment: Abstract class for imaging experiments |
| pixelNames-method | ImagingExperiment: Abstract class for imaging experiments |
| pixelNames-method | SparseImagingExperiment: Pixel-sparse imaging experiments |
| pixelNames-method | Legacy classes and methods in Cardinal |
| pixelNames-methods | ImagingExperiment: Abstract class for imaging experiments |
| pixelNames<- | ImagingExperiment: Abstract class for imaging experiments |
| pixelNames<--method | ImagingExperiment: Abstract class for imaging experiments |
| pixelNames<--method | SparseImagingExperiment: Pixel-sparse imaging experiments |
| pixelNames<--method | Legacy classes and methods in Cardinal |
| pixels | SparseImagingExperiment: Pixel-sparse imaging experiments |
| pixels-method | MSImagingExperiment: Mass spectrometry imaging experiments |
| pixels-method | SparseImagingExperiment: Pixel-sparse imaging experiments |
| pixels-method | Legacy classes and methods in Cardinal |
| pixels-methods | SparseImagingExperiment: Pixel-sparse imaging experiments |
| pixelSize | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| pixelSize-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| pixelSize-method | Legacy classes and methods in Cardinal |
| 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 | Legacy classes and methods in Cardinal |
| positionArray-method | Legacy classes and methods in Cardinal |
| positionArray<- | Legacy classes and methods in Cardinal |
| positionArray<--method | Legacy classes and methods in Cardinal |
| PositionDataFrame | PositionDataFrame: data frame with spatial position metadata |
| PositionDataFrame-class | PositionDataFrame: data frame with spatial position metadata |
| predict-method | Principal components analysis |
| predict-method | Partial least squares |
| predict-method | Spatially-aware shrunken centroid clustering and classification |
| preproc-method | SparseImagingExperiment: Pixel-sparse imaging experiments |
| preproc-method | Legacy classes and methods in Cardinal |
| preproc<--method | Legacy classes and methods in Cardinal |
| presetImageDef | Simulate a mass spectrum or MS imaging experiment |
| print.summary.CrossValidated | Apply cross-validation to imaging analyses |
| print.summary.iSet | Legacy classes and methods in Cardinal |
| 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 | Legacy classes and methods in Cardinal |
| processingData-method | SparseImagingExperiment: Pixel-sparse imaging experiments |
| processingData-method | Legacy classes and methods in Cardinal |
| processingData-methods | Legacy classes and methods in Cardinal |
| processingData<- | Legacy classes and methods in Cardinal |
| processingData<--method | SparseImagingExperiment: Pixel-sparse imaging experiments |
| processingData<--method | Legacy classes and methods in Cardinal |
| protocolData-method | Legacy classes and methods in Cardinal |
| protocolData<--method | Legacy classes and methods in Cardinal |
| pubMedIds-method | Legacy classes and methods in Cardinal |
| pubMedIds<--method | Legacy classes and methods in Cardinal |
| pull-method | MSImagingExperiment: Mass spectrometry imaging experiments |
| pull-method | MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments |
| pull-method | SparseImagingExperiment: Pixel-sparse imaging experiments |
| range-method | AnnotatedImage: Optical images with annotations |
| rbind-method | AnnotatedImagingExperiment: Mass spectrometry imaging experiments |
| rbind-method | ImageList: Abstract image data list |
| rbind-method | ImagingExperiment: Abstract class for imaging experiments |
| rbind-method | ImagingResult: Results of statistical analysis of imaging experiments |
| rbind-method | MSImagingExperiment: Mass spectrometry imaging experiments |
| rbind-method | MassDataFrame: data frame with mass-to-charge ratio metadata |
| rbind-method | PositionDataFrame: data frame with spatial position metadata |
| rbind-method | SparseImagingExperiment: Pixel-sparse imaging experiments |
| rbind-method | XDataFrame: DataFrame with eXtra metadata columns |
| rbind-method | Legacy classes and methods in Cardinal |
| readAnalyze | Read mass spectrometry imaging data files |
| readImzML | Read mass spectrometry imaging data files |
| readMSIData | Read mass spectrometry imaging data files |
| reduceBaseline | Reduce the baseline for an imaging dataset |
| reduceBaseline-method | Reduce the baseline for an imaging dataset |
| reduceBaseline-methods | Reduce the baseline for an imaging dataset |
| reduceBaseline.locmin | Reduce the baseline for an imaging dataset |
| reduceBaseline.median | Reduce the baseline for an imaging dataset |
| reduceDimension | Legacy classes and methods in Cardinal |
| reduceDimension-method | Legacy classes and methods in Cardinal |
| reduceDimension-methods | Legacy classes and methods in Cardinal |
| reduceDimension.bin | Legacy classes and methods in Cardinal |
| reduceDimension.peaks | Legacy classes and methods in Cardinal |
| reduceDimension.resample | Legacy classes and methods in Cardinal |
| regeneratePositions | Legacy classes and methods in Cardinal |
| regeneratePositions-method | Legacy classes and methods in Cardinal |
| resolution | PositionDataFrame: data frame with spatial position metadata |
| resolution-method | AnnotatedImage: Optical images with annotations |
| resolution-method | AnnotatedImagingExperiment: Mass spectrometry imaging experiments |
| 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 | AnnotatedImage: Optical images with annotations |
| resolution<--method | MSImagingExperiment: Mass spectrometry imaging experiments |
| resolution<--method | MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments |
| resolution<--method | MassDataFrame: data frame with mass-to-charge ratio metadata |
| resolution<--method | PositionDataFrame: data frame with spatial position metadata |
| resolution<--method | SparseImagingExperiment: Pixel-sparse imaging experiments |
| resultData | ImagingResult: Results of statistical analysis of imaging experiments |
| resultData-method | ImagingResult: Results of statistical analysis of imaging experiments |
| resultData-method | Legacy classes and methods in Cardinal |
| resultData<- | ImagingResult: Results of statistical analysis of imaging experiments |
| resultData<--method | ImagingResult: Results of statistical analysis of imaging experiments |
| resultData<--method | Legacy classes and methods in Cardinal |
| resultNames | ImagingResult: Results of statistical analysis of imaging experiments |
| resultNames-method | ImagingResult: Results of statistical analysis of imaging experiments |
| resultNames<- | ImagingResult: Results of statistical analysis of imaging experiments |
| ResultSet | Legacy classes and methods in Cardinal |
| ResultSet-class | Legacy classes and methods in Cardinal |
| risk.colors | Color palettes for imaging |
| rownames-method | Legacy classes and methods in Cardinal |
| rownames<--method | Legacy classes and methods in Cardinal |
| 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 |
| sampleNames | ImagingExperiment: Abstract class for imaging experiments |
| sampleNames-method | ImagingExperiment: Abstract class for imaging experiments |
| sampleNames-method | Legacy classes and methods in Cardinal |
| sampleNames-methods | ImagingExperiment: Abstract class for imaging experiments |
| sampleNames<- | ImagingExperiment: Abstract class for imaging experiments |
| sampleNames<--method | ImagingExperiment: Abstract class for imaging experiments |
| sampleNames<--method | Legacy classes and methods in Cardinal |
| samples-method | Legacy classes and methods in Cardinal |
| scanDirection | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| scanDirection-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| scanDirection-method | Legacy classes and methods in Cardinal |
| scanPattern | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| scanPattern-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| scanPattern-method | Legacy classes and methods in Cardinal |
| scanPolarity | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| scanPolarity-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| scanPolarity-method | Legacy classes and methods in Cardinal |
| scans-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| scanType | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| scanType-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| scanType-method | Legacy classes and methods in Cardinal |
| 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 | Deprecated functions and methods in Cardinal |
| select.SparseImagingExperiment | Deprecated functions and methods in Cardinal |
| selectROI | Select regions-of-interest of an imaging dataset |
| selectROI-method | Select regions-of-interest of an imaging dataset |
| selectROI-methods | Select regions-of-interest of an imaging dataset |
| setCardinalBPPARAM | Mass spectrometry imaging tools |
| setCardinalDelayProc | Mass spectrometry imaging tools |
| setCardinalNumBlocks | Mass spectrometry imaging tools |
| setCardinalVerbose | Mass spectrometry imaging tools |
| setup.layout | Plot a signal from the feature data of an imaging dataset |
| show-method | AnnotatedImagingExperiment: Mass spectrometry imaging experiments |
| show-method | ImageList: Abstract image data list |
| show-method | ImagingExperiment: Abstract class for imaging experiments |
| show-method | ImagingResult: Results of statistical analysis of imaging experiments |
| show-method | MSImagingExperiment: Mass spectrometry imaging experiments |
| show-method | SparseImagingExperiment: Pixel-sparse imaging experiments |
| show-method | XDataFrame: DataFrame with eXtra metadata columns |
| show-method | Legacy classes and methods in Cardinal |
| showNames | XDataFrame: DataFrame with eXtra metadata columns |
| showNames-method | MassDataFrame: data frame with mass-to-charge ratio metadata |
| showNames-method | PositionDataFrame: data frame with spatial position metadata |
| showNames-method | XDataFrame: DataFrame with eXtra metadata columns |
| SImageData | Legacy classes and methods in Cardinal |
| SImageData-class | Legacy classes and methods in Cardinal |
| SImageSet | Legacy classes and methods in Cardinal |
| SImageSet-class | Legacy classes and methods in Cardinal |
| SimpleImageArrayList-class | ImageList: Abstract image data list |
| SimpleImageList-class | ImageList: Abstract image data list |
| simulateImage | Simulate a mass spectrum or MS imaging experiment |
| simulateSpectrum | Simulate a mass spectrum or MS imaging experiment |
| slice | Slice an image |
| slice-method | Slice an image |
| slice.SparseImagingExperiment | Deprecated functions and methods in Cardinal |
| smooth | Smooth the signals of a imaging dataset |
| smooth-method | Smooth the signals of a imaging dataset |
| smooth-methods | Smooth the signals of a imaging dataset |
| smoothing | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| smoothing-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| smoothing-method | Legacy classes and methods in Cardinal |
| smoothing<- | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| smoothing<--method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| smoothing<--method | Legacy classes and methods in Cardinal |
| 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 | Legacy classes and methods in Cardinal |
| softwareName-method | Legacy classes and methods in Cardinal |
| softwareVersion | Legacy classes and methods in Cardinal |
| softwareVersion-method | Legacy classes and methods in Cardinal |
| sort-method | XDataFrame: DataFrame with eXtra metadata columns |
| SparseImagingExperiment | SparseImagingExperiment: Pixel-sparse imaging experiments |
| SparseImagingExperiment-class | SparseImagingExperiment: Pixel-sparse imaging experiments |
| SparseImagingResult | ImagingResult: Results of statistical analysis of imaging experiments |
| SparseImagingResult-class | ImagingResult: Results of statistical analysis of imaging experiments |
| spatialApply | 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 | Legacy classes and methods in Cardinal |
| specimenOrigin-method | Legacy classes and methods in Cardinal |
| specimenType | Legacy classes and methods in Cardinal |
| specimenType-method | Legacy classes and methods in Cardinal |
| spectra | MSImagingExperiment: Mass spectrometry imaging experiments |
| spectra-method | MSImagingExperiment: Mass spectrometry imaging experiments |
| spectra-method | Legacy classes and methods in Cardinal |
| spectra-methods | MSImagingExperiment: Mass spectrometry imaging experiments |
| spectra<- | MSImagingExperiment: Mass spectrometry imaging experiments |
| spectra<--method | MSImagingExperiment: Mass spectrometry imaging experiments |
| spectra<--method | Legacy classes and methods in Cardinal |
| spectraData | MSImagingExperiment: Mass spectrometry imaging experiments |
| spectraData-method | MSImagingExperiment: Mass spectrometry imaging experiments |
| spectraData-methods | MSImagingExperiment: Mass spectrometry imaging experiments |
| spectraData<- | MSImagingExperiment: Mass spectrometry imaging experiments |
| spectraData<--method | MSImagingExperiment: Mass spectrometry imaging experiments |
| spectrumRepresentation | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| spectrumRepresentation-method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| spectrumRepresentation-method | Legacy classes and methods in Cardinal |
| spectrumRepresentation<- | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| spectrumRepresentation<--method | MSImagingInfo: Mass spectrometry imaging metadata for imzML conversion |
| spectrumRepresentation<--method | Legacy classes and methods in Cardinal |
| stainingMethod | Legacy classes and methods in Cardinal |
| stainingMethod-method | Legacy classes and methods in Cardinal |
| standardizeRuns | Legacy classes and methods in Cardinal |
| standardizeRuns-method | Legacy classes and methods in Cardinal |
| standardizeRuns-methods | Legacy classes and methods in Cardinal |
| standardizeRuns.sum | Legacy classes and methods in Cardinal |
| storageMode-method | Legacy classes and methods in Cardinal |
| storageMode<--method | Legacy classes and methods in Cardinal |
| subset-method | Subsetting |
| subsetFeatures | Subsetting |
| subsetPixels | Subsetting |
| summarise | Deprecated functions and methods in Cardinal |
| summarise.MSImagingExperiment | Deprecated functions and methods in Cardinal |
| summarise.SparseImagingExperiment | Deprecated functions and methods in Cardinal |
| summarize | Deprecated functions and methods in Cardinal |
| summarizeFeatures | Calculating summary statistics |
| summarizePixels | Calculating summary statistics |
| summary-method | Principal components analysis |
| summary-method | Partial least squares |
| summary-method | Apply cross-validation to imaging analyses |
| summary-method | Legacy classes and methods in Cardinal |
| 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 |
| tissueThickness | Legacy classes and methods in Cardinal |
| tissueThickness-method | Legacy classes and methods in Cardinal |
| tissueWash | Legacy classes and methods in Cardinal |
| tissueWash-method | Legacy classes and methods in Cardinal |
| tolerance-method | MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments |
| tolerance<--method | MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments |
| topFeatures | Top-ranked features from imaging analysis results |
| topFeatures-method | Top-ranked features from imaging analysis results |
| topFeatures-methods | Top-ranked features from imaging analysis results |
| ungroup | Deprecated functions and methods in Cardinal |
| varLabels-method | Legacy classes and methods in Cardinal |
| varLabels<--method | Legacy classes and methods in Cardinal |
| varMetadata-method | Legacy classes and methods in Cardinal |
| varMetadata<--method | Legacy classes and methods in Cardinal |
| viridis | Objects exported from other packages |
| width-method | AnnotatedImage: Optical images with annotations |
| width-method | AnnotatedImagingExperiment: Mass spectrometry imaging experiments |
| width<--method | AnnotatedImage: Optical images with annotations |
| 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 |
| XDataFrame | XDataFrame: DataFrame with eXtra metadata columns |
| XDataFrame-class | XDataFrame: DataFrame with eXtra metadata columns |
| $-method | ImagingExperiment: Abstract class for imaging experiments |
| $-method | ImagingResult: Results of statistical analysis of imaging experiments |
| $-method | Legacy classes and methods in Cardinal |
| $<--method | ImagingExperiment: Abstract class for imaging experiments |
| $<--method | XDataFrame: DataFrame with eXtra metadata columns |
| $<--method | Legacy classes and methods in Cardinal |
| %>% | Objects exported from other packages |
| [-method | AnnotatedImagingExperiment: Mass spectrometry imaging experiments |
| [-method | ImageList: Abstract image data list |
| [-method | ImagingExperiment: Abstract class for imaging experiments |
| [-method | ImagingResult: Results of statistical analysis of imaging experiments |
| [-method | MSContinuousImagingExperiment: "Continuous" mass spectrometry imaging experiments |
| [-method | MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments |
| [-method | MassDataFrame: data frame with mass-to-charge ratio metadata |
| [-method | PositionDataFrame: data frame with spatial position metadata |
| [-method | SparseImagingExperiment: Pixel-sparse imaging experiments |
| [-method | XDataFrame: DataFrame with eXtra metadata columns |
| [-method | Legacy classes and methods in Cardinal |
| [<--method | ImageList: Abstract image data list |
| [<--method | ImagingExperiment: Abstract class for imaging experiments |
| [<--method | SparseImagingExperiment: Pixel-sparse imaging experiments |
| [<--method | Legacy classes and methods in Cardinal |
| [[-method | ImageList: Abstract image data list |
| [[-method | ImagingExperiment: Abstract class for imaging experiments |
| [[-method | ImagingResult: Results of statistical analysis of imaging experiments |
| [[-method | Legacy classes and methods in Cardinal |
| [[<--method | ImageList: Abstract image data list |
| [[<--method | ImagingExperiment: Abstract class for imaging experiments |
| [[<--method | ImagingResult: Results of statistical analysis of imaging experiments |
| [[<--method | MSContinuousImagingExperiment: "Continuous" mass spectrometry imaging experiments |
| [[<--method | MSProcessedImagingExperiment: "Processed" mass spectrometry imaging experiments |
| [[<--method | XDataFrame: DataFrame with eXtra metadata columns |
| [[<--method | Legacy classes and methods in Cardinal |