Man pages for Cardinal
A mass spectrometry imaging toolbox for statistical analysis

aggregate-methodsCalculating summary statistics
AnnotatedImage-classAnnotatedImage: Optical images with annotations
AnnotatedImagingExperiment-classAnnotatedImagingExperiment: Mass spectrometry imaging...
Cardinal-packageMass spectrometry imaging tools
colocalized-methodsColocalized features
colors-functionsColor palettes for imaging
crossValidate-methodsApply cross-validation to imaging analyses
defunctDefunct functions and methods in Cardinal
deprecatedDeprecated functions and methods in Cardinal
findNeighbors-methodsFind spatial neighbors and spatial weightst
ImageList-classImageList: Abstract image data list
image-methodsPlot an image of the pixel data of an imaging dataset
ImagingExperiment-classImagingExperiment: Abstract class for imaging experiments
ImagingResult-classImagingResult: Results of statistical analysis of imaging...
internalInternal utilities for Cardinal
legacyLegacy classes and methods in Cardinal
MassDataFrame-classMassDataFrame: data frame with mass-to-charge ratio metadata
meansTest-methodsLinear model-based testing for summarized imaging experiments
MSContinuousImagingExperiment-classMSContinuousImagingExperiment: "Continuous" mass spectrometry...
MSImagingExperiment-classMSImagingExperiment: Mass spectrometry imaging experiments
MSImagingInfo-classMSImagingInfo: Mass spectrometry imaging metadata for imzML...
MSProcessedImagingExperiment-classMSProcessedImagingExperiment: "Processed" mass spectrometry...
mzAlign-methodsMass align an imaging dataset
mzBin-methodsMass bin an imaging dataset
mzFilter-methodsFilter the features of an imaging dataset by intensity
mz-methodsManipulate mass-to-charge-ratio values
normalize-methodsNormalize an imaging dataset
PCA-methodsPrincipal components analysis
peakAlign-methodsPeak align an imaging dataset
peakBin-methodsPeak bin an imaging dataset
peakPick-methodsPeak pick an imaging dataset
pixelApply-methodsApply functions over imaging datasets
plot-methodsPlot a signal from the feature data of an imaging dataset
PLS-methodsPartial least squares
PositionDataFrame-classPositionDataFrame: data frame with spatial position metadata
process-methodsDelayed Processing of Imaging Datasets
readMSIDataRead mass spectrometry imaging data files
reduceBaseline-methodsReduce the baseline for an imaging dataset
reexportsObjects exported from other packages
selectROI-methodsSelect regions-of-interest of an imaging dataset
simulateSpectrumSimulate a mass spectrum or MS imaging experiment
slice-methodsSlice an image
smoothSignal-methodsSmooth the signals of a imaging dataset
SparseImagingExperiment-classSparseImagingExperiment: Pixel-sparse imaging experiments
spatialDGMM-methodsSpatially-aware Dirichlet Gaussian mixture model
spatialFastmap-methodsSpatially-aware FastMap projection
spatialKMeans-methodsSpatially-aware k-means clustering
spatialShrunkenCentroids-methodsSpatially-aware shrunken centroid clustering and...
subset-methodsSubsetting
topFeatures-methodsTop-ranked features from imaging analysis results
writeMSIDataWrite mass spectrometry imaging data files
XDataFrame-classXDataFrame: DataFrame with eXtra metadata columns
Cardinal documentation built on Nov. 8, 2020, 11:10 p.m.