A mass spectrometry imaging toolbox for statistical analysis
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Documentation for package ‘Cardinal’ version 3.11.0
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A B C D E F G H I J K L M N O P R S T V W X misc
| Cardinal-package | Mass spectrometry imaging tools |
-- A --
| addProcessing-method | Apply queued processing to spectra |
| addShape | Simulate a mass spectrum or MS imaging experiment |
| aggregate-method | Deprecated and defunct objects in Cardinal |
| alpha.colors | Deprecated and defunct objects in Cardinal |
| as_facets | Re-exported objects from Cardinal |
| as_layers | Re-exported objects from Cardinal |
-- B --
| baselineReduction | Deprecated and defunct objects in Cardinal |
| baselineReduction<- | Deprecated and defunct objects in Cardinal |
| bin | Bin spectra |
| bin-method | Bin spectra |
| bw.colors | Deprecated and defunct objects in Cardinal |
-- C --
| c-method | MSImagingArrays: MS imaging data with arbitrary m/z values |
| c-method | SpectraArrays: List of spectra arrays |
| c-method | SpectralImagingArrays: Spectral imaging data with arbitrary domain |
| Cardinal | Mass spectrometry imaging tools |
| cbind-method | MSImagingExperiment: MS imaging data with shared m/z values |
| cbind-method | SpectraArrays: List of spectra arrays |
| cbind-method | SpectralImagingArrays: Spectral imaging data with arbitrary domain |
| cbind-method | SpectralImagingExperiment: Spectral imaging data with shared domain |
| cbind-method | XDataFrame: Extended data frame with key columns |
| centroided-method | MSImagingExperiment: MS imaging data with shared m/z values |
| centroided<--method | MSImagingExperiment: MS imaging data with shared m/z values |
| class:Hashmat | Deprecated and defunct objects in Cardinal |
| class:IAnnotatedDataFrame | Deprecated and defunct objects in Cardinal |
| class:ImageData | Deprecated and defunct objects in Cardinal |
| class:iSet | Deprecated and defunct objects in Cardinal |
| class:MassDataFrame | MassDataFrame: Extended data frame with key columns |
| class:MeansTest | Linear model-based testing for summarized imaging experiments |
| class:MIAPE-Imaging | Deprecated and defunct objects in Cardinal |
| class:MSImageData | Deprecated and defunct objects in Cardinal |
| class:MSImageProcess | Deprecated and defunct objects in Cardinal |
| class:MSImageSet | Deprecated and defunct objects in Cardinal |
| class:MSImagingArrays | MSImagingArrays: MS imaging data with arbitrary m/z values |
| class:MSImagingExperiment | MSImagingExperiment: MS imaging data with shared m/z values |
| class:PositionDataFrame | PositionDataFrame: Extended data frame with key columns |
| class:ResultSet | Deprecated and defunct objects in Cardinal |
| class:ResultsList | ResultsList: List of modeling results |
| class:SImageData | Deprecated and defunct objects in Cardinal |
| class:SImageSet | Deprecated and defunct objects in Cardinal |
| class:SpatialCV | Cross-validation for spectral imaging data |
| class:SpatialDGMM | Spatially-aware Dirichlet Gaussian mixture model |
| class:SpatialFastmap | Spatially-aware FastMap projection |
| class:SpatialKMeans | Spatially-aware K-means clustering |
| class:SpatialNMF | Non-negative matrix factorization |
| class:SpatialOPLS | Partial least squares (projection to latent structures) |
| class:SpatialPCA | Principal components analysis |
| class:SpatialPLS | Partial least squares (projection to latent structures) |
| class:SpatialResults | SpatialResults: Modeling results with spatial metadata |
| class:SpatialShrunkenCentroids | Spatially-aware shrunken centroid clustering and classification |
| class:SpectraArrays | SpectraArrays: List of spectra arrays |
| class:SpectralImagingArrays | SpectralImagingArrays: Spectral imaging data with arbitrary domain |
| class:SpectralImagingData | SpectralImagingData: Abstract class for spectral imaging data |
| class:SpectralImagingExperiment | SpectralImagingExperiment: Spectral imaging data with shared domain |
| class:XDataFrame | XDataFrame: Extended data frame with key columns |
| class:XDFrame | XDataFrame: Extended data frame with key columns |
| classNameForDisplay-method | XDataFrame: Extended data frame with key columns |
| coef-method | Partial least squares (projection to latent structures) |
| coerce-method | MSImagingExperiment: MS imaging data with shared m/z values |
| coerce-method | MassDataFrame: Extended data frame with key columns |
| coerce-method | PositionDataFrame: Extended data frame with key columns |
| coerce-method | SpectraArrays: List of spectra arrays |
| coerce-method | XDataFrame: Extended data frame with key columns |
| coerce-method | Read mass spectrometry imaging data files |
| col.map | Deprecated and defunct objects in Cardinal |
| colMeans-method | Summarize a spectral imaging dataset |
| colnames-method | SpectralImagingExperiment: Spectral imaging data with shared domain |
| colnames<--method | SpectralImagingExperiment: Spectral imaging data with shared domain |
| colocalized | Colocalized features |
| colocalized-method | Colocalized features |
| color.map | Deprecated and defunct objects in Cardinal |
| colStats-method | Summarize a spectral imaging dataset |
| colSums-method | Summarize a spectral imaging dataset |
| combine-method | SpectraArrays: List of spectra arrays |
| combine-method | SpectralImagingArrays: Spectral imaging data with arbitrary domain |
| combine-method | SpectralImagingExperiment: Spectral imaging data with shared domain |
| convertMSImagingArrays2Experiment | Read mass spectrometry imaging data files |
| convertMSImagingExperiment2Arrays | Read mass spectrometry imaging data files |
| coord | PositionDataFrame: Extended data frame with key columns |
| coord-method | PositionDataFrame: Extended data frame with key columns |
| coord-method | SpatialResults: Modeling results with spatial metadata |
| coord-method | SpectralImagingData: Abstract class for spectral imaging data |
| coord<- | PositionDataFrame: Extended data frame with key columns |
| coord<--method | PositionDataFrame: Extended data frame with key columns |
| coord<--method | SpatialResults: Modeling results with spatial metadata |
| coord<--method | SpectralImagingData: Abstract class for spectral imaging data |
| coordNames | PositionDataFrame: Extended data frame with key columns |
| coordNames-method | PositionDataFrame: Extended data frame with key columns |
| coordNames-method | SpatialResults: Modeling results with spatial metadata |
| coordNames-method | SpectralImagingData: Abstract class for spectral imaging data |
| coordNames<- | PositionDataFrame: Extended data frame with key columns |
| coordNames<--method | PositionDataFrame: Extended data frame with key columns |
| coordNames<--method | SpatialResults: Modeling results with spatial metadata |
| coordNames<--method | SpectralImagingData: Abstract class for spectral imaging data |
| coregister | Colocalized features |
| cpal | Re-exported objects from Cardinal |
| cpals | Re-exported objects from Cardinal |
| crossValidate | Cross-validation for spectral imaging data |
| cvApply | Deprecated and defunct objects in Cardinal |
-- D --
| darkmode | Deprecated and defunct objects in Cardinal |
| deprecated | Deprecated and defunct objects in Cardinal |
| dim-method | SpectraArrays: List of spectra arrays |
| dim-method | SpectralImagingArrays: Spectral imaging data with arbitrary domain |
| dim-method | SpectralImagingExperiment: Spectral imaging data with shared domain |
| discrete.colors | Deprecated and defunct objects in Cardinal |
| divergent.colors | Deprecated and defunct objects in Cardinal |
| dpal | Re-exported objects from Cardinal |
| dpals | Re-exported objects from Cardinal |
| dropkeys | XDataFrame: Extended data frame with key columns |
| dropkeys-method | XDataFrame: Extended data frame with key columns |
-- E --
| estimateDomain | Estimate shared domain |
| estimateReferenceMz | Estimate shared domain |
| estimateReferencePeaks | Estimate shared domain |
| experimentData-method | MSImagingExperiment: MS imaging data with shared m/z values |
| experimentData<--method | MSImagingExperiment: MS imaging data with shared m/z values |
-- F --
| fData-method | SpatialResults: Modeling results with spatial metadata |
| fData-method | SpectralImagingExperiment: Spectral imaging data with shared domain |
| fData<--method | SpatialResults: Modeling results with spatial metadata |
| fData<--method | SpectralImagingExperiment: Spectral imaging data with shared domain |
| featureApply | Deprecated and defunct objects in Cardinal |
| featureApply-method | Deprecated and defunct objects in Cardinal |
| featureData-method | SpatialResults: Modeling results with spatial metadata |
| featureData-method | SpectralImagingExperiment: Spectral imaging data with shared domain |
| featureData<--method | SpatialResults: Modeling results with spatial metadata |
| featureData<--method | SpectralImagingExperiment: Spectral imaging data with shared domain |
| featureNames-method | SpatialResults: Modeling results with spatial metadata |
| featureNames-method | SpectralImagingExperiment: Spectral imaging data with shared domain |
| featureNames<--method | SpatialResults: Modeling results with spatial metadata |
| featureNames<--method | SpectralImagingExperiment: Spectral imaging data with shared domain |
| features | Find feature indices |
| features-method | Find feature indices |
| fetch-method | SpectraArrays: List of spectra arrays |
| fetch-method | SpectralImagingData: Abstract class for spectral imaging data |
| findNeighbors | Find spatial neighbors |
| findNeighbors-method | Find spatial neighbors |
| fitted-method | ResultsList: List of modeling results |
| fitted-method | Cross-validation for spectral imaging data |
| fitted-method | Partial least squares (projection to latent structures) |
| fitted-method | SpatialResults: Modeling results with spatial metadata |
| fitted-method | Spatially-aware shrunken centroid clustering and classification |
| flash-method | SpectraArrays: List of spectra arrays |
| flash-method | SpectralImagingData: Abstract class for spectral imaging data |
-- G --
| getCardinalBPPARAM | Mass spectrometry imaging tools |
| getCardinalChunksize | Mass spectrometry imaging tools |
| getCardinalLogger | Mass spectrometry imaging tools |
| getCardinalNChunks | Mass spectrometry imaging tools |
| getCardinalNumBlocks | Deprecated and defunct objects in Cardinal |
| getCardinalParallel | Mass spectrometry imaging tools |
| getCardinalSerialize | Mass spectrometry imaging tools |
| getCardinalVerbose | Mass spectrometry imaging tools |
| gradient.colors | Deprecated and defunct objects in Cardinal |
| gridded | Deprecated and defunct objects in Cardinal |
| gridded<- | Deprecated and defunct objects in Cardinal |
-- H --
| Hashmat | Deprecated and defunct objects in Cardinal |
| Hashmat-class | Deprecated and defunct objects in Cardinal |
| height | Deprecated and defunct objects in Cardinal |
| height<- | Deprecated and defunct objects in Cardinal |
-- I --
| IAnnotatedDataFrame | Deprecated and defunct objects in Cardinal |
| IAnnotatedDataFrame-class | Deprecated and defunct objects in Cardinal |
| iData | Deprecated and defunct objects in Cardinal |
| iData-method | Deprecated and defunct objects in Cardinal |
| iData<- | Deprecated and defunct objects in Cardinal |
| iData<--method | Deprecated and defunct objects in Cardinal |
| image | Plot images from a spectral imaging dataset |
| image-method | ResultsList: List of modeling results |
| image-method | Cross-validation for spectral imaging data |
| image-method | Spatially-aware Dirichlet Gaussian mixture model |
| image-method | Spatially-aware FastMap projection |
| image-method | Spatially-aware K-means clustering |
| image-method | Non-negative matrix factorization |
| image-method | Principal components analysis |
| image-method | Partial least squares (projection to latent structures) |
| image-method | SpatialResults: Modeling results with spatial metadata |
| image-method | Spatially-aware shrunken centroid clustering and classification |
| image-method | Plot images from a spectral imaging dataset |
| image3D | Plot images from a spectral imaging dataset |
| image3D-method | Plot images from a spectral imaging dataset |
| ImageData | Deprecated and defunct objects in Cardinal |
| ImageData-class | Deprecated and defunct objects in Cardinal |
| instrumentVendor | Deprecated and defunct objects in Cardinal |
| intensity-method | MSImagingArrays: MS imaging data with arbitrary m/z values |
| intensity-method | MSImagingExperiment: MS imaging data with shared m/z values |
| intensity.colors | Deprecated and defunct objects in Cardinal |
| intensity<--method | MSImagingArrays: MS imaging data with arbitrary m/z values |
| intensity<--method | MSImagingExperiment: MS imaging data with shared m/z values |
| intensityData | Deprecated and defunct objects in Cardinal |
| intensityData<- | Deprecated and defunct objects in Cardinal |
| ionizationType | Deprecated and defunct objects in Cardinal |
| is3D | Deprecated and defunct objects in Cardinal |
| is3D-method | PositionDataFrame: Extended data frame with key columns |
| is3D-method | SpectralImagingData: Abstract class for spectral imaging data |
| isCentroided-method | MSImagingExperiment: MS imaging data with shared m/z values |
| iSet | Deprecated and defunct objects in Cardinal |
| iSet-class | Deprecated and defunct objects in Cardinal |
-- J --
| jet.colors | Deprecated and defunct objects in Cardinal |
-- K --
| keys | XDataFrame: Extended data frame with key columns |
| keys-method | XDataFrame: Extended data frame with key columns |
| keys<- | XDataFrame: Extended data frame with key columns |
| keys<--method | XDataFrame: Extended data frame with key columns |
-- L --
| length-method | SpatialResults: Modeling results with spatial metadata |
| length-method | SpectraArrays: List of spectra arrays |
| length-method | SpectralImagingArrays: Spectral imaging data with arbitrary domain |
| length-method | SpectralImagingExperiment: Spectral imaging data with shared domain |
| lightmode | Deprecated and defunct objects in Cardinal |
| lineScanDirection | Deprecated and defunct objects in Cardinal |
| logLik-method | Spatially-aware Dirichlet Gaussian mixture model |
| logLik-method | Spatially-aware shrunken centroid clustering and classification |
-- M --
| makeFactor | Select regions-of-interest in an image |
| massAnalyzerType | Deprecated and defunct objects in Cardinal |
| MassDataFrame | MassDataFrame: Extended data frame with key columns |
| MassDataFrame-class | MassDataFrame: Extended data frame with key columns |
| matrixApplication | Deprecated and defunct objects in Cardinal |
| MeansTest | Linear model-based testing for summarized imaging experiments |
| meansTest | Linear model-based testing for summarized imaging experiments |
| MeansTest-class | Linear model-based testing for summarized imaging experiments |
| meansTest-method | Linear model-based testing for summarized imaging experiments |
| MIAPE-Imaging | Deprecated and defunct objects in Cardinal |
| MIAPE-Imaging-class | Deprecated and defunct objects in Cardinal |
| modelData | SpatialResults: Modeling results with spatial metadata |
| modelData-method | SpatialResults: Modeling results with spatial metadata |
| modelData<- | SpatialResults: Modeling results with spatial metadata |
| modelData<--method | SpatialResults: Modeling results with spatial metadata |
| msiInfo | Deprecated and defunct objects in Cardinal |
| MSImageData | Deprecated and defunct objects in Cardinal |
| MSImageData-class | Deprecated and defunct objects in Cardinal |
| MSImageProcess | Deprecated and defunct objects in Cardinal |
| MSImageProcess-class | Deprecated and defunct objects in Cardinal |
| MSImageSet | Deprecated and defunct objects in Cardinal |
| MSImageSet-class | Deprecated and defunct objects in Cardinal |
| MSImagingArrays | MSImagingArrays: MS imaging data with arbitrary m/z values |
| MSImagingArrays-class | MSImagingArrays: MS imaging data with arbitrary m/z values |
| MSImagingExperiment | MSImagingExperiment: MS imaging data with shared m/z values |
| MSImagingExperiment-class | MSImagingExperiment: MS imaging data with shared m/z values |
| mz-method | MSImagingArrays: MS imaging data with arbitrary m/z values |
| mz-method | MSImagingExperiment: MS imaging data with shared m/z values |
| mz-method | MassDataFrame: Extended data frame with key columns |
| mz<--method | MSImagingArrays: MS imaging data with arbitrary m/z values |
| mz<--method | MSImagingExperiment: MS imaging data with shared m/z values |
| mz<--method | MassDataFrame: Extended data frame with key columns |
| mzAlign | Deprecated and defunct objects in Cardinal |
| mzAlign-method | Deprecated and defunct objects in Cardinal |
| mzBin | Deprecated and defunct objects in Cardinal |
| mzBin-method | Deprecated and defunct objects in Cardinal |
| mzData | Deprecated and defunct objects in Cardinal |
| mzData<- | Deprecated and defunct objects in Cardinal |
| mzFilter | Deprecated and defunct objects in Cardinal |
| mzFilter-method | Deprecated and defunct objects in Cardinal |
-- N --
| names-method | SpatialResults: Modeling results with spatial metadata |
| names-method | SpectraArrays: List of spectra arrays |
| names-method | SpectralImagingArrays: Spectral imaging data with arbitrary domain |
| names-method | SpectralImagingExperiment: Spectral imaging data with shared domain |
| names<--method | SpectraArrays: List of spectra arrays |
| names<--method | SpectralImagingArrays: Spectral imaging data with arbitrary domain |
| names<--method | SpectralImagingExperiment: Spectral imaging data with shared domain |
| names<--method | XDataFrame: Extended data frame with key columns |
| NMF | Non-negative matrix factorization |
| NMF-method | Non-negative matrix factorization |
| normalization | Deprecated and defunct objects in Cardinal |
| normalization<- | Deprecated and defunct objects in Cardinal |
| normalize | Normalize spectra |
| normalize-method | Normalize spectra |
| nrun-method | PositionDataFrame: Extended data frame with key columns |
| nrun-method | SpatialResults: Modeling results with spatial metadata |
| nrun-method | SpectralImagingData: Abstract class for spectral imaging data |
-- O --
| OPLS | Partial least squares (projection to latent structures) |
| OPLS-method | Partial least squares (projection to latent structures) |
-- P --
| PCA | Principal components analysis |
| PCA-method | Principal components analysis |
| pData-method | SpatialResults: Modeling results with spatial metadata |
| pData-method | SpectralImagingData: Abstract class for spectral imaging data |
| pData<--method | SpatialResults: Modeling results with spatial metadata |
| pData<--method | SpectralImagingData: Abstract class for spectral imaging data |
| peakAlign | Align peaks across spectra |
| peakAlign-method | Align peaks across spectra |
| peakBin | Deprecated and defunct objects in Cardinal |
| peakData | Deprecated and defunct objects in Cardinal |
| peakData<- | Deprecated and defunct objects in Cardinal |
| peakFilter | Deprecated and defunct objects in Cardinal |
| peakFilter-method | Deprecated and defunct objects in Cardinal |
| peakPick | Peak pick spectra |
| peakPick-method | Peak pick spectra |
| peakPicking | Deprecated and defunct objects in Cardinal |
| peakPicking<- | Deprecated and defunct objects in Cardinal |
| peakProcess | Process peaks in mass spectra |
| peakProcess-method | Process peaks in mass spectra |
| pixelApply | Deprecated and defunct objects in Cardinal |
| pixelApply-method | Deprecated and defunct objects in Cardinal |
| pixelData | SpectralImagingData: Abstract class for spectral imaging data |
| pixelData-method | SpatialResults: Modeling results with spatial metadata |
| pixelData-method | SpectralImagingData: Abstract class for spectral imaging data |
| pixelData<- | SpectralImagingData: Abstract class for spectral imaging data |
| pixelData<--method | SpatialResults: Modeling results with spatial metadata |
| pixelData<--method | SpectralImagingData: Abstract class for spectral imaging data |
| pixelNames | SpectralImagingData: Abstract class for spectral imaging data |
| pixelNames-method | SpatialResults: Modeling results with spatial metadata |
| pixelNames-method | SpectralImagingData: Abstract class for spectral imaging data |
| pixelNames<- | SpectralImagingData: Abstract class for spectral imaging data |
| pixelNames<--method | SpatialResults: Modeling results with spatial metadata |
| pixelNames<--method | SpectralImagingData: Abstract class for spectral imaging data |
| pixels | Find pixel indices |
| pixels-method | Find pixel indices |
| pixelSize | Deprecated and defunct objects in Cardinal |
| plot | Plot spectra from a spectral imaging dataset |
| plot-image | Plot images from a spectral imaging dataset |
| plot-method | Linear model-based testing for summarized imaging experiments |
| plot-method | ResultsList: List of modeling results |
| plot-method | Spatially-aware Dirichlet Gaussian mixture model |
| plot-method | Spatially-aware FastMap projection |
| plot-method | Spatially-aware K-means clustering |
| plot-method | Non-negative matrix factorization |
| plot-method | Principal components analysis |
| plot-method | Partial least squares (projection to latent structures) |
| plot-method | SpatialResults: Modeling results with spatial metadata |
| plot-method | Spatially-aware shrunken centroid clustering and classification |
| plot-method | Plot spectra from a spectral imaging dataset |
| plot-spectra | Plot spectra from a spectral imaging dataset |
| PLS | Partial least squares (projection to latent structures) |
| PLS-method | Partial least squares (projection to latent structures) |
| PositionDataFrame | PositionDataFrame: Extended data frame with key columns |
| PositionDataFrame-class | PositionDataFrame: Extended data frame with key columns |
| predict-method | ResultsList: List of modeling results |
| predict-method | Spatially-aware FastMap projection |
| predict-method | Non-negative matrix factorization |
| predict-method | Principal components analysis |
| predict-method | Partial least squares (projection to latent structures) |
| predict-method | Spatially-aware shrunken centroid clustering and classification |
| presetImageDef | Simulate a mass spectrum or MS imaging experiment |
| process | Apply queued processing to spectra |
| process-method | Apply queued processing to spectra |
| processingData-method | SpectralImagingData: Abstract class for spectral imaging data |
| processingData<--method | SpectralImagingData: Abstract class for spectral imaging data |
-- R --
| rbind-method | MSImagingExperiment: MS imaging data with shared m/z values |
| rbind-method | SpectraArrays: List of spectra arrays |
| rbind-method | SpectralImagingArrays: Spectral imaging data with arbitrary domain |
| rbind-method | SpectralImagingExperiment: Spectral imaging data with shared domain |
| rbind-method | XDataFrame: Extended data frame with key columns |
| readAnalyze | Read mass spectrometry imaging data files |
| readImzML | Read mass spectrometry imaging data files |
| readMSIData | Read mass spectrometry imaging data files |
| recalibrate | Recalibrate spectra |
| recalibrate-method | Recalibrate spectra |
| reduceBaseline | Reduce baselines in spectra |
| reduceBaseline-method | Reduce baselines in spectra |
| reexports | Re-exported objects from Cardinal |
| reset | Apply queued processing to spectra |
| residuals-method | Partial least squares (projection to latent structures) |
| resolution | Deprecated and defunct objects in Cardinal |
| resolution<- | Deprecated and defunct objects in Cardinal |
| resultData | Deprecated and defunct objects in Cardinal |
| resultData<- | Deprecated and defunct objects in Cardinal |
| resultNames | Deprecated and defunct objects in Cardinal |
| resultNames<- | Deprecated and defunct objects in Cardinal |
| ResultSet | Deprecated and defunct objects in Cardinal |
| ResultSet-class | Deprecated and defunct objects in Cardinal |
| ResultsList | ResultsList: List of modeling results |
| ResultsList-class | ResultsList: List of modeling results |
| risk.colors | Deprecated and defunct objects in Cardinal |
| rowMeans-method | Summarize a spectral imaging dataset |
| rownames-method | SpectralImagingExperiment: Spectral imaging data with shared domain |
| rownames<--method | SpectralImagingExperiment: Spectral imaging data with shared domain |
| rowStats-method | Summarize a spectral imaging dataset |
| rowSums-method | Summarize a spectral imaging dataset |
| run | PositionDataFrame: Extended data frame with key columns |
| run-method | PositionDataFrame: Extended data frame with key columns |
| run-method | SpatialResults: Modeling results with spatial metadata |
| run-method | SpectralImagingData: Abstract class for spectral imaging data |
| run<- | PositionDataFrame: Extended data frame with key columns |
| run<--method | PositionDataFrame: Extended data frame with key columns |
| run<--method | SpatialResults: Modeling results with spatial metadata |
| run<--method | SpectralImagingData: Abstract class for spectral imaging data |
| runNames | PositionDataFrame: Extended data frame with key columns |
| runNames-method | PositionDataFrame: Extended data frame with key columns |
| runNames-method | SpatialResults: Modeling results with spatial metadata |
| runNames-method | SpectralImagingData: Abstract class for spectral imaging data |
| runNames<- | PositionDataFrame: Extended data frame with key columns |
| runNames<--method | PositionDataFrame: Extended data frame with key columns |
| runNames<--method | SpatialResults: Modeling results with spatial metadata |
| runNames<--method | SpectralImagingData: Abstract class for spectral imaging data |
-- S --
| saveCardinalLog | Mass spectrometry imaging tools |
| scanDirection | Deprecated and defunct objects in Cardinal |
| scanPattern | Deprecated and defunct objects in Cardinal |
| scanPolarity | Deprecated and defunct objects in Cardinal |
| scanType | Deprecated and defunct objects in Cardinal |
| segmentationTest | Linear model-based testing for summarized imaging experiments |
| selectROI | Select regions-of-interest in an image |
| selectROI-method | Select regions-of-interest in an image |
| setCardinalBPPARAM | Mass spectrometry imaging tools |
| setCardinalChunksize | Mass spectrometry imaging tools |
| setCardinalLogger | Mass spectrometry imaging tools |
| setCardinalNChunks | Mass spectrometry imaging tools |
| setCardinalNumBlocks | Deprecated and defunct objects in Cardinal |
| setCardinalParallel | Mass spectrometry imaging tools |
| setCardinalSerialize | Mass spectrometry imaging tools |
| setCardinalVerbose | Mass spectrometry imaging tools |
| show-method | MSImagingArrays: MS imaging data with arbitrary m/z values |
| show-method | MSImagingExperiment: MS imaging data with shared m/z values |
| show-method | ResultsList: List of modeling results |
| show-method | SpatialResults: Modeling results with spatial metadata |
| show-method | SpectraArrays: List of spectra arrays |
| show-method | SpectralImagingArrays: Spectral imaging data with arbitrary domain |
| show-method | SpectralImagingData: Abstract class for spectral imaging data |
| show-method | SpectralImagingExperiment: Spectral imaging data with shared domain |
| show-method | XDataFrame: Extended data frame with key columns |
| SImageData | Deprecated and defunct objects in Cardinal |
| SImageData-class | Deprecated and defunct objects in Cardinal |
| SImageSet | Deprecated and defunct objects in Cardinal |
| SImageSet-class | Deprecated and defunct objects in Cardinal |
| simulateImage | Simulate a mass spectrum or MS imaging experiment |
| simulateSpectra | Simulate a mass spectrum or MS imaging experiment |
| simulateSpectrum | Deprecated and defunct objects in Cardinal |
| slice | Deprecated and defunct objects in Cardinal |
| sliceImage | Slice an image |
| smooth | Smooth spectra |
| smooth-method | Smooth spectra |
| smoothing | Deprecated and defunct objects in Cardinal |
| smoothing<- | Deprecated and defunct objects in Cardinal |
| smoothSignal | Deprecated and defunct objects in Cardinal |
| smoothSignal-method | Deprecated and defunct objects in Cardinal |
| SnowfastParam | Re-exported objects from Cardinal |
| spatialApply | Deprecated and defunct objects in Cardinal |
| spatialApply-method | Deprecated and defunct objects in Cardinal |
| SpatialCV | Cross-validation for spectral imaging data |
| SpatialCV-class | Cross-validation for spectral imaging data |
| SpatialDGMM | Spatially-aware Dirichlet Gaussian mixture model |
| spatialDGMM | Spatially-aware Dirichlet Gaussian mixture model |
| SpatialDGMM-class | Spatially-aware Dirichlet Gaussian mixture model |
| spatialDGMM-method | Spatially-aware Dirichlet Gaussian mixture model |
| spatialDists | Calculate spatially-smoothed distances |
| spatialDists-method | Calculate spatially-smoothed distances |
| SpatialFastmap | Spatially-aware FastMap projection |
| spatialFastmap | Spatially-aware FastMap projection |
| SpatialFastmap-class | Spatially-aware FastMap projection |
| spatialFastmap-method | Spatially-aware FastMap projection |
| SpatialKMeans | Spatially-aware K-means clustering |
| spatialKMeans | Spatially-aware K-means clustering |
| SpatialKMeans-class | Spatially-aware K-means clustering |
| spatialKMeans-method | Spatially-aware K-means clustering |
| SpatialNMF | Non-negative matrix factorization |
| SpatialNMF-class | Non-negative matrix factorization |
| SpatialOPLS | Partial least squares (projection to latent structures) |
| SpatialOPLS-class | Partial least squares (projection to latent structures) |
| SpatialPCA | Principal components analysis |
| SpatialPCA-class | Principal components analysis |
| SpatialPLS | Partial least squares (projection to latent structures) |
| SpatialPLS-class | Partial least squares (projection to latent structures) |
| SpatialResults | SpatialResults: Modeling results with spatial metadata |
| SpatialResults-class | SpatialResults: Modeling results with spatial metadata |
| SpatialShrunkenCentroids | Spatially-aware shrunken centroid clustering and classification |
| spatialShrunkenCentroids | Spatially-aware shrunken centroid clustering and classification |
| SpatialShrunkenCentroids-class | Spatially-aware shrunken centroid clustering and classification |
| spatialShrunkenCentroids-method | Spatially-aware shrunken centroid clustering and classification |
| spatialWeights | Calculate spatial weights |
| spatialWeights-method | Calculate spatial weights |
| spectra-method | SpectralImagingData: Abstract class for spectral imaging data |
| spectra<--method | SpectralImagingData: Abstract class for spectral imaging data |
| SpectraArrays | SpectraArrays: List of spectra arrays |
| SpectraArrays-class | SpectraArrays: List of spectra arrays |
| spectraData-method | SpectralImagingData: Abstract class for spectral imaging data |
| spectraData<--method | SpectralImagingData: Abstract class for spectral imaging data |
| SpectralImagingArrays | SpectralImagingArrays: Spectral imaging data with arbitrary domain |
| SpectralImagingArrays-class | SpectralImagingArrays: Spectral imaging data with arbitrary domain |
| SpectralImagingData | SpectralImagingData: Abstract class for spectral imaging data |
| SpectralImagingData-class | SpectralImagingData: Abstract class for spectral imaging data |
| SpectralImagingExperiment | SpectralImagingExperiment: Spectral imaging data with shared domain |
| SpectralImagingExperiment-class | SpectralImagingExperiment: Spectral imaging data with shared domain |
| spectraNames-method | SpectralImagingData: Abstract class for spectral imaging data |
| spectraNames<--method | SpectralImagingData: Abstract class for spectral imaging data |
| spectrapply | Apply functions over spectra |
| spectrapply-method | Apply functions over spectra |
| spectraVariables-method | SpectralImagingData: Abstract class for spectral imaging data |
| spectrumRepresentation | Deprecated and defunct objects in Cardinal |
| spectrumRepresentation<- | Deprecated and defunct objects in Cardinal |
| subset-method | Subset a spectral imaging dataset |
| subsetFeatures | Subset a spectral imaging dataset |
| subsetPixels | Subset a spectral imaging dataset |
| summarizeFeatures | Summarize a spectral imaging dataset |
| summarizePixels | Summarize a spectral imaging dataset |
-- T --
| topFeatures | Spatially-aware shrunken centroid clustering and classification |
| topFeatures-method | Linear model-based testing for summarized imaging experiments |
| topFeatures-method | ResultsList: List of modeling results |
| topFeatures-method | Spatially-aware K-means clustering |
| topFeatures-method | Partial least squares (projection to latent structures) |
| topFeatures-method | Spatially-aware shrunken centroid clustering and classification |
-- V --
| vizi_engine | Mass spectrometry imaging tools |
| vizi_par | Mass spectrometry imaging tools |
| vizi_style | Mass spectrometry imaging tools |
| vm_used-method | SpectraArrays: List of spectra arrays |
-- W --
| writeAnalyze | Write mass spectrometry imaging data files |
| writeAnalyze-method | Write mass spectrometry imaging data files |
| writeImzML | Write mass spectrometry imaging data files |
| writeImzML-method | Write mass spectrometry imaging data files |
| writeMSIData | Write mass spectrometry imaging data files |
-- X --
| XDataFrame | XDataFrame: Extended data frame with key columns |
| XDataFrame-class | XDataFrame: Extended data frame with key columns |
| XDFrame | XDataFrame: Extended data frame with key columns |
| XDFrame-class | XDataFrame: Extended data frame with key columns |
-- misc --
| $-method | SpatialResults: Modeling results with spatial metadata |
| $-method | SpectraArrays: List of spectra arrays |
| $-method | SpectralImagingData: Abstract class for spectral imaging data |
| $<--method | SpectraArrays: List of spectra arrays |
| $<--method | SpectralImagingData: Abstract class for spectral imaging data |
| $<--method | XDataFrame: Extended data frame with key columns |
| [-method | MassDataFrame: Extended data frame with key columns |
| [-method | PositionDataFrame: Extended data frame with key columns |
| [-method | SpectraArrays: List of spectra arrays |
| [-method | SpectralImagingArrays: Spectral imaging data with arbitrary domain |
| [-method | SpectralImagingExperiment: Spectral imaging data with shared domain |
| [-method | XDataFrame: Extended data frame with key columns |
| [<--method | SpectraArrays: List of spectra arrays |
| [<--method | SpectralImagingArrays: Spectral imaging data with arbitrary domain |
| [<--method | SpectralImagingExperiment: Spectral imaging data with shared domain |
| [<--method | XDataFrame: Extended data frame with key columns |
| [[-method | SpatialResults: Modeling results with spatial metadata |
| [[-method | SpectraArrays: List of spectra arrays |
| [[-method | SpectralImagingData: Abstract class for spectral imaging data |
| [[<--method | SpectraArrays: List of spectra arrays |
| [[<--method | SpectralImagingData: Abstract class for spectral imaging data |
| [[<--method | XDataFrame: Extended data frame with key columns |