Package: Cardinal 3.9.0
Kylie Ariel Bemis
Cardinal: A mass spectrometry imaging toolbox for statistical analysis
Implements statistical & computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification.
Authors:
Cardinal_3.9.0.tar.gz
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Cardinal_3.9.0.tgz(r-4.4-any)Cardinal_3.7.5.tgz(r-4.3-any)
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Cardinal.pdf |Cardinal.html✨
Cardinal/json (API)
NEWS
| # Install 'Cardinal' in R: |
| install.packages('Cardinal', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/kuwisdelu/cardinal/issues
On BioConductor:Cardinal-3.9.0(bioc 3.21)Cardinal-3.8.0(bioc 3.20)
softwareinfrastructureproteomicslipidomicsmassspectrometryimagingmassspectrometryimmunooncologynormalizationclusteringclassificationregression
Last updated 22 days agofrom:8b2a58caa6. Checks:OK: 3 WARNING: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 13 2024 |
| R-4.5-win | WARNING | Nov 13 2024 |
| R-4.5-linux | WARNING | Nov 13 2024 |
| R-4.4-win | WARNING | Nov 13 2024 |
| R-4.4-mac | WARNING | Nov 13 2024 |
| R-4.3-win | OK | Oct 15 2024 |
| R-4.3-mac | OK | Oct 15 2024 |
Exports:abstractaddProcessingaddShapeaggregatealpha.colorsannotatedDataFrameFromas_facetsas_layersas.arrayas.data.frameas.matrixbaselineReductionbaselineReduction<-binbw.colorscbindcentroidedcentroided<-coefcoercecol.mapcolMeanscolnamescolnames<-colocalizedcolor.mapcolStatscolSumscombineconvertMSImagingArrays2ExperimentconvertMSImagingExperiment2Arrayscoordcoord<-coordNamescoordNames<-coregistercpalcpalscrossValidatecvApplydarkmodedimsdiscrete.colorsdivergent.colorsdomaindomain<-dpaldpalsdropkeysestimateDomainestimateReferenceMzestimateReferencePeaksexperimentDataexperimentData<-expinfofDatafData<-featureApplyfeatureDatafeatureData<-featureNamesfeatureNames<-featuresfetchfindNeighborsfittedflashfvarLabelsfvarLabels<-fvarMetadatafvarMetadata<-getCardinalBPPARAMgetCardinalChunksizegetCardinalLoggergetCardinalNChunksgetCardinalNumBlocksgetCardinalParallelgetCardinalSerializegetCardinalVerbosegradient.colorsgriddedgridded<-heightheight<-iDataiData<-imageimage3DimageDataimageData<-initializeinstrumentModelinstrumentVendorintensityintensity.colorsintensity<-intensityDataintensityData<-ionizationTypeis3DisCentroidedjet.colorskeyskeys<-lightmodelineScanDirectionlogLikmakeFactormassAnalyzerTypeMassDataFramematrixApplicationmeansTestmodelDatamodelData<-msiInfoMSImagingArraysMSImagingExperimentmzmz<-mzAlignmzBinmzDatamzData<-mzFilterNMFnormalizationnormalization<-normalizenotesnotes<-nrunOPLSotherInfoPCApDatapData<-peakAlignpeakBinpeakDatapeakData<-peakFilterpeakPickpeakPickingpeakPicking<-peakProcesspeakspeaks<-phenoDataphenoData<-pixelApplypixelDatapixelData<-pixelNamespixelNames<-pixelspixelSizeplotPLSPositionDataFramepredictpreprocpreproc<-presetImageDefprocessprotocolDataprotocolData<-pubMedIdspubMedIds<-rbindreadAnalyzereadImzMLreadMSIDatarecalibratereduceBaselineresetresidualsresolutionresolution<-resultDataresultData<-resultNamesresultNames<-ResultsListrisk.colorsrowMeansrownamesrownames<-rowStatsrowSumsrunrun<-runNamesrunNames<-sampleNamessampleNames<-samplessaveCardinalLogscanDirectionscanPatternscanPolarityscanTypesegmentationTestselectROIsetCardinalBPPARAMsetCardinalChunksizesetCardinalLoggersetCardinalNChunkssetCardinalNumBlockssetCardinalParallelsetCardinalSerializesetCardinalVerbosesimulateImagesimulateSpectrasimulateSpectrumslicesliceImagesmoothsmoothingsmoothing<-smoothSignalSnowfastParamspatialApplyspatialDGMMspatialDistsspatialFastmapspatialKMeansSpatialResultsspatialShrunkenCentroidsspatialWeightsspectraspectra<-SpectraArraysSpectralImagingArraysSpectralImagingExperimentspectrapplyspectrumRepresentationspectrumRepresentation<-storageModestorageMode<-subsetsubsetFeaturessubsetPixelssummarizeFeaturessummarizePixelstopFeaturesvarLabelsvarLabels<-varMetadatavarMetadata<-vizi_enginevizi_parvizi_stylewidthwidth<-writeAnalyzewriteImzMLwriteMSIDataXDataFrame
Dependencies:abindbase64encBHBiobaseBiocGenericsBiocParallelbitopsbslibcachemCardinalIOclicodetoolscpp11digestEBImageevaluatefastmapfftwtoolsfontawesomeformatRfsfutile.loggerfutile.optionsgenericsgluehighrhtmltoolshtmlwidgetsirlbajpegjquerylibjsonliteknitrlambda.rlatticelifecyclelocfitMatrixmattermemoisemimenlmeontologyIndexpngProtGenericsR6rappdirsRCurlrlangrmarkdownS4Vectorssasssnowtifftinytexxfunyaml
Cardinal 3: User guide for mass spectrometry imaging analysis
Rendered fromCardinal3-guide.Rmdusingknitr::rmarkdownon Nov 13 2024.Last update: 2024-10-26
Started: 2024-04-09
Cardinal 3: Statistical methods for mass spectrometry imaging
Rendered fromCardinal3-stats.Rmdusingknitr::rmarkdownon Nov 13 2024.Last update: 2024-09-08
Started: 2024-04-09
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Mass spectrometry imaging tools | Cardinal-package Cardinal getCardinalBPPARAM getCardinalChunksize getCardinalLogger getCardinalNChunks getCardinalParallel getCardinalSerialize getCardinalVerbose saveCardinalLog setCardinalBPPARAM setCardinalChunksize setCardinalLogger setCardinalNChunks setCardinalParallel setCardinalSerialize setCardinalVerbose vizi_engine vizi_par vizi_style |
| Bin spectra | bin bin,MSImagingArrays-method bin,MSImagingExperiment-method bin,SpectralImagingArrays-method bin,SpectralImagingExperiment-method |
| Colocalized features | colocalized colocalized,MSImagingExperiment-method colocalized,SpatialDGMM-method colocalized,SpectralImagingExperiment-method coregister |
| Deprecated and defunct objects in Cardinal | aggregate,SpectralImagingExperiment-method alpha.colors baselineReduction baselineReduction<- bw.colors class:Hashmat class:IAnnotatedDataFrame class:ImageData class:iSet class:MIAPE-Imaging class:MSImageData class:MSImageProcess class:MSImageSet class:ResultSet class:SImageData class:SImageSet col.map color.map cvApply darkmode deprecated discrete.colors divergent.colors featureApply featureApply,SpectralImagingExperiment-method getCardinalNumBlocks gradient.colors gridded gridded<- Hashmat Hashmat-class height height<- IAnnotatedDataFrame IAnnotatedDataFrame-class iData iData,ANY-method iData<- iData<-,ANY-method ImageData ImageData-class instrumentVendor intensity.colors intensityData intensityData<- ionizationType is3D iSet iSet-class jet.colors lightmode lineScanDirection massAnalyzerType matrixApplication MIAPE-Imaging MIAPE-Imaging-class msiInfo MSImageData MSImageData-class MSImageProcess MSImageProcess-class MSImageSet MSImageSet-class mzAlign mzAlign,MSImagingExperiment,missing-method mzAlign,MSImagingExperiment,numeric-method mzBin mzBin,MSImagingExperiment,missing-method mzBin,MSImagingExperiment,numeric-method mzData mzData<- mzFilter mzFilter,MSImagingExperiment-method normalization normalization<- peakBin peakData peakData<- peakFilter peakFilter,MSImagingExperiment-method peakPicking peakPicking<- pixelApply pixelApply,SpectralImagingExperiment-method pixelSize resolution resolution<- resultData resultData<- resultNames resultNames<- ResultSet ResultSet-class risk.colors scanDirection scanPattern scanPolarity scanType setCardinalNumBlocks SImageData SImageData-class SImageSet SImageSet-class simulateSpectrum slice smoothing smoothing<- smoothSignal smoothSignal,SpectralImagingExperiment-method spatialApply spatialApply,SpectralImagingExperiment-method spectrumRepresentation spectrumRepresentation<- |
| Estimate shared domain | estimateDomain estimateReferenceMz estimateReferencePeaks |
| Find feature indices | features features,MSImagingExperiment-method features,SpectralImagingExperiment-method |
| Find spatial neighbors | findNeighbors findNeighbors,ANY-method findNeighbors,PositionDataFrame-method findNeighbors,SpectralImagingData-method |
| MassDataFrame: Extended data frame with key columns | class:MassDataFrame coerce,DFrame,MassDataFrame-method MassDataFrame MassDataFrame-class mz,MassDataFrame-method mz<-,MassDataFrame-method [,MassDataFrame,ANY,ANY,ANY-method |
| Linear model-based testing for summarized imaging experiments | class:MeansTest MeansTest meansTest meansTest,ANY-method meansTest,SpatialDGMM-method meansTest,SpectralImagingExperiment-method MeansTest-class plot,MeansTest,missing-method segmentationTest topFeatures,MeansTest-method |
| MSImagingArrays: MS imaging data with arbitrary m/z values | c,MSImagingArrays-method class:MSImagingArrays intensity,MSImagingArrays-method intensity<-,MSImagingArrays-method MSImagingArrays MSImagingArrays-class mz,MSImagingArrays-method mz<-,MSImagingArrays-method show,MSImagingArrays-method |
| MSImagingExperiment: MS imaging data with shared m/z values | cbind,MSImagingExperiment-method centroided,MSImagingExperiment_OR_Arrays-method centroided<-,MSImagingExperiment_OR_Arrays-method class:MSImagingExperiment coerce,MSImageSet,MSImagingExperiment-method experimentData,MSImagingExperiment_OR_Arrays-method experimentData<-,MSImagingExperiment_OR_Arrays,ANY-method intensity,MSImagingExperiment-method intensity<-,MSImagingExperiment-method isCentroided,MSImagingExperiment_OR_Arrays-method MSImagingExperiment MSImagingExperiment-class mz,missing-method mz,MSImagingExperiment-method mz<-,MSImagingExperiment-method rbind,MSImagingExperiment-method show,MSImagingExperiment-method |
| Normalize spectra | normalize normalize,MSImagingExperiment_OR_Arrays-method normalize,SpectralImagingData-method |
| Align peaks across spectra | peakAlign peakAlign,MSImagingArrays-method peakAlign,MSImagingExperiment-method peakAlign,SpectralImagingArrays-method peakAlign,SpectralImagingExperiment-method |
| Peak pick spectra | peakPick peakPick,MSImagingArrays-method peakPick,MSImagingExperiment-method peakPick,SpectralImagingData-method |
| Process peaks in mass spectra | peakProcess peakProcess,MSImagingExperiment_OR_Arrays-method |
| Find pixel indices | pixels pixels,SpectralImagingArrays-method pixels,SpectralImagingData-method pixels,SpectralImagingExperiment-method |
| Plot images from a spectral imaging dataset | image image,MSImagingExperiment-method image,PositionDataFrame-method image,SpectralImagingExperiment-method image3D image3D,MSImagingExperiment-method plot-image |
| Plot spectra from a spectral imaging dataset | plot plot,MSImagingArrays,formula-method plot,MSImagingArrays,missing-method plot,MSImagingArrays,numeric-method plot,MSImagingExperiment,character-method plot,MSImagingExperiment,formula-method plot,MSImagingExperiment,missing-method plot,MSImagingExperiment,numeric-method plot,SpectralImagingArrays,formula-method plot,SpectralImagingArrays,missing-method plot,SpectralImagingArrays,numeric-method plot,SpectralImagingExperiment,character-method plot,SpectralImagingExperiment,formula-method plot,SpectralImagingExperiment,missing-method plot,SpectralImagingExperiment,numeric-method plot,XDataFrame,character-method plot,XDataFrame,formula-method plot,XDataFrame,missing-method plot-spectra |
| PositionDataFrame: Extended data frame with key columns | class:PositionDataFrame coerce,DFrame,PositionDataFrame-method coord coord,PositionDataFrame-method coord<- coord<-,PositionDataFrame-method coordNames coordNames,PositionDataFrame-method coordNames<- coordNames<-,PositionDataFrame-method is3D,PositionDataFrame-method nrun,PositionDataFrame-method PositionDataFrame PositionDataFrame-class run run,PositionDataFrame-method run<- run<-,PositionDataFrame-method runNames runNames,PositionDataFrame-method runNames<- runNames<-,PositionDataFrame-method [,PositionDataFrame,ANY,ANY,ANY-method |
| Apply queued processing to spectra | addProcessing,SpectralImagingData-method process process,MSImagingArrays-method process,MSImagingExperiment-method process,SpectralImagingArrays-method process,SpectralImagingExperiment-method reset |
| Read mass spectrometry imaging data files | coerce,MSImagingArrays,MSImagingExperiment-method coerce,MSImagingExperiment,MSImagingArrays-method convertMSImagingArrays2Experiment convertMSImagingExperiment2Arrays readAnalyze readImzML readMSIData |
| Recalibrate spectra | recalibrate recalibrate,MSImagingExperiment_OR_Arrays-method recalibrate,SpectralImagingData-method |
| Reduce baselines in spectra | reduceBaseline reduceBaseline,SpectralImagingData-method |
| Re-exported objects from Cardinal | as_facets as_layers cpal cpals dpal dpals reexports SnowfastParam |
| ResultsList: List of modeling results | class:ResultsList fitted,ResultsList-method image,ResultsList-method plot,ResultsList,ANY-method plot,ResultsList,missing-method predict,ResultsList-method ResultsList ResultsList-class show,ResultsList-method topFeatures,ResultsList-method |
| Select regions-of-interest in an image | makeFactor selectROI selectROI,SpectralImagingExperiment-method |
| Simulate a mass spectrum or MS imaging experiment | addShape presetImageDef simulateImage simulateSpectra |
| Slice an image | sliceImage |
| Smooth spectra | smooth smooth,SpectralImagingData-method |
| Cross-validation for spectral imaging data | class:SpatialCV crossValidate fitted,SpatialCV-method image,SpatialCV-method SpatialCV SpatialCV-class |
| Spatially-aware Dirichlet Gaussian mixture model | class:SpatialDGMM image,SpatialDGMM-method logLik,SpatialDGMM-method plot,SpatialDGMM,missing-method SpatialDGMM spatialDGMM spatialDGMM,ANY-method spatialDGMM,SpectralImagingExperiment-method SpatialDGMM-class |
| Calculate spatially-smoothed distances | spatialDists spatialDists,ANY-method spatialDists,PositionDataFrame-method spatialDists,SpectralImagingExperiment-method |
| Spatially-aware FastMap projection | class:SpatialFastmap image,SpatialFastmap-method plot,SpatialFastmap,missing-method predict,SpatialFastmap-method SpatialFastmap spatialFastmap spatialFastmap,ANY-method spatialFastmap,SpectralImagingExperiment-method SpatialFastmap-class |
| Spatially-aware K-means clustering | class:SpatialKMeans image,SpatialKMeans-method plot,SpatialKMeans,missing-method SpatialKMeans spatialKMeans spatialKMeans,ANY-method spatialKMeans,SpectralImagingExperiment-method SpatialKMeans-class topFeatures,SpatialKMeans-method |
| Non-negative matrix factorization | class:SpatialNMF image,SpatialNMF-method NMF NMF,ANY-method NMF,SpectralImagingExperiment-method plot,SpatialNMF,missing-method predict,SpatialNMF-method SpatialNMF SpatialNMF-class |
| Principal components analysis | class:SpatialPCA image,SpatialPCA-method PCA PCA,ANY-method PCA,SpectralImagingExperiment-method plot,SpatialPCA,missing-method predict,SpatialPCA-method SpatialPCA SpatialPCA-class |
| Partial least squares (projection to latent structures) | class:SpatialOPLS class:SpatialPLS coef,SpatialOPLS-method fitted,SpatialOPLS-method fitted,SpatialPLS-method image,SpatialOPLS-method image,SpatialPLS-method OPLS OPLS,ANY-method OPLS,SpectralImagingExperiment-method plot,SpatialOPLS,missing-method plot,SpatialPLS,missing-method PLS PLS,ANY-method PLS,SpectralImagingExperiment-method predict,SpatialOPLS-method predict,SpatialPLS-method residuals,SpatialOPLS-method SpatialOPLS SpatialOPLS-class SpatialPLS SpatialPLS-class topFeatures,SpatialOPLS-method topFeatures,SpatialPLS-method |
| SpatialResults: Modeling results with spatial metadata | $,SpatialResults-method class:SpatialResults coord,SpatialResults-method coord<-,SpatialResults-method coordNames,SpatialResults-method coordNames<-,SpatialResults-method fData,SpatialResults-method fData<-,SpatialResults,ANY-method featureData,SpatialResults-method featureData<-,SpatialResults,ANY-method featureNames,SpatialResults-method featureNames<-,SpatialResults-method fitted,SpatialResults-method image,SpatialResults-method length,SpatialResults-method modelData modelData,SpatialResults-method modelData<- modelData<-,SpatialResults-method names,SpatialResults-method nrun,SpatialResults-method pData,SpatialResults-method pData<-,SpatialResults,ANY-method pixelData,SpatialResults-method pixelData<-,SpatialResults-method pixelNames,SpatialResults-method pixelNames<-,SpatialResults-method plot,SpatialResults,ANY-method run,SpatialResults-method run<-,SpatialResults-method runNames,SpatialResults-method runNames<-,SpatialResults-method show,SpatialResults-method SpatialResults SpatialResults-class [[,SpatialResults-method |
| Spatially-aware shrunken centroid clustering and classification | class:SpatialShrunkenCentroids fitted,SpatialShrunkenCentroids-method image,SpatialShrunkenCentroids-method logLik,SpatialShrunkenCentroids-method plot,SpatialShrunkenCentroids,missing-method predict,SpatialShrunkenCentroids-method SpatialShrunkenCentroids spatialShrunkenCentroids spatialShrunkenCentroids,ANY,ANY-method spatialShrunkenCentroids,ANY,missing-method spatialShrunkenCentroids,SpectralImagingExperiment,ANY-method spatialShrunkenCentroids,SpectralImagingExperiment,missing-method SpatialShrunkenCentroids-class topFeatures topFeatures,SpatialShrunkenCentroids-method |
| Calculate spatial weights | spatialWeights spatialWeights,ANY-method spatialWeights,PositionDataFrame-method spatialWeights,SpectralImagingExperiment-method |
| SpectraArrays: List of spectra arrays | $,SpectraArrays-method $<-,SpectraArrays-method c,SpectraArrays-method cbind,SpectraArrays-method class:SpectraArrays coerce,list,SpectraArrays-method coerce,SimpleList,SpectraArrays-method coerce,SpectraArrays,list-method coerce,SpectraArrays,SimpleList-method combine,SpectraArrays,ANY-method dim,SpectraArrays-method fetch,SpectraArrays-method flash,SpectraArrays-method length,SpectraArrays-method names,SpectraArrays-method names<-,SpectraArrays-method rbind,SpectraArrays-method show,SpectraArrays-method SpectraArrays SpectraArrays-class vm_used,SpectraArrays-method [,SpectraArrays,ANY,ANY,ANY-method [<-,SpectraArrays,ANY,ANY,ANY-method [[,SpectraArrays-method [[<-,SpectraArrays-method |
| SpectralImagingArrays: Spectral imaging data with arbitrary domain | c,SpectralImagingArrays-method cbind,SpectralImagingArrays-method class:SpectralImagingArrays combine,SpectralImagingArrays,ANY-method dim,SpectralImagingArrays-method length,SpectralImagingArrays-method names,SpectralImagingArrays-method names<-,SpectralImagingArrays-method rbind,SpectralImagingArrays-method show,SpectralImagingArrays-method SpectralImagingArrays SpectralImagingArrays-class [,SpectralImagingArrays,ANY,ANY,ANY-method [<-,SpectralImagingArrays,ANY,ANY,ANY-method |
| SpectralImagingData: Abstract class for spectral imaging data | $,SpectralImagingData-method $<-,SpectralImagingData-method class:SpectralImagingData coord,SpectralImagingData-method coord<-,SpectralImagingData-method coordNames,SpectralImagingData-method coordNames<-,SpectralImagingData-method fetch,SpectralImagingData-method flash,SpectralImagingData-method is3D,SpectralImagingData-method nrun,SpectralImagingData-method pData,SpectralImagingData-method pData<-,SpectralImagingData,ANY-method pixelData pixelData,SpectralImagingData-method pixelData<- pixelData<-,SpectralImagingData-method pixelNames pixelNames,SpectralImagingData-method pixelNames<- pixelNames<-,SpectralImagingData-method processingData,SpectralImagingData-method processingData<-,SpectralImagingData-method run,SpectralImagingData-method run<-,SpectralImagingData-method runNames,SpectralImagingData-method runNames<-,SpectralImagingData-method show,SpectralImagingData-method spectra,SpectralImagingData-method spectra<-,SpectralImagingData-method spectraData,SpectralImagingData-method spectraData<-,SpectralImagingData-method SpectralImagingData SpectralImagingData-class spectraNames,SpectralImagingData-method spectraNames<-,SpectralImagingData-method spectraVariables,SpectralImagingData-method [[,SpectralImagingData-method [[<-,SpectralImagingData-method |
| SpectralImagingExperiment: Spectral imaging data with shared domain | cbind,SpectralImagingExperiment-method class:SpectralImagingExperiment colnames,SpectralImagingExperiment-method colnames<-,SpectralImagingExperiment-method combine,SpectralImagingExperiment,ANY-method dim,SpectralImagingExperiment-method fData,SpectralImagingExperiment-method fData<-,SpectralImagingExperiment,ANY-method featureData,SpectralImagingExperiment-method featureData<-,SpectralImagingExperiment,ANY-method featureNames,SpectralImagingExperiment-method featureNames<-,SpectralImagingExperiment-method length,SpectralImagingExperiment-method names,SpectralImagingExperiment-method names<-,SpectralImagingExperiment-method rbind,SpectralImagingExperiment-method rownames,SpectralImagingExperiment-method rownames<-,SpectralImagingExperiment-method show,SpectralImagingExperiment-method SpectralImagingExperiment SpectralImagingExperiment-class [,SpectralImagingExperiment,ANY,ANY,ANY-method [<-,SpectralImagingExperiment,ANY,ANY,ANY-method |
| Apply functions over spectra | spectrapply spectrapply,SpectralImagingArrays-method spectrapply,SpectralImagingExperiment-method |
| Subset a spectral imaging dataset | subset,SpectralImagingArrays-method subset,SpectralImagingExperiment-method subsetFeatures subsetPixels |
| Summarize a spectral imaging dataset | colMeans,SpectralImagingExperiment-method colStats,SpectralImagingExperiment-method colSums,SpectralImagingExperiment-method rowMeans,SpectralImagingExperiment-method rowStats,SpectralImagingExperiment-method rowSums,SpectralImagingExperiment-method summarizeFeatures summarizePixels |
| Write mass spectrometry imaging data files | writeAnalyze writeAnalyze,MSImagingExperiment-method writeAnalyze,SpectralImagingExperiment-method writeImzML writeImzML,MSImagingExperiment_OR_Arrays-method writeMSIData |
| XDataFrame: Extended data frame with key columns | $<-,XDataFrame-method cbind,XDataFrame-method class:XDataFrame class:XDFrame classNameForDisplay,XDFrame-method coerce,DataFrame,XDataFrame-method dropkeys dropkeys,XDataFrame-method keys keys,XDataFrame-method keys<- keys<-,XDataFrame-method names<-,XDataFrame-method rbind,XDataFrame-method show,XDataFrame-method XDataFrame XDataFrame-class XDFrame XDFrame-class [,XDataFrame,ANY,ANY,ANY-method [<-,XDataFrame,ANY,ANY,ANY-method [[<-,XDataFrame-method |
