Man pages for Cardinal
A mass spectrometry imaging toolbox for statistical analysis
| aggregate-methods | Calculating summary statistics |
| AnnotatedImage-class | AnnotatedImage: Optical images with annotations |
| AnnotatedImagingExperiment-class | AnnotatedImagingExperiment: Mass spectrometry imaging... |
| Cardinal-package | Mass spectrometry imaging tools |
| colocalized-methods | Colocalized features |
| colors-functions | Color palettes for imaging |
| crossValidate-methods | Apply cross-validation to imaging analyses |
| defunct | Defunct functions and methods in Cardinal |
| deprecated | Deprecated functions and methods in Cardinal |
| findNeighbors-methods | Find spatial neighbors and spatial weightst |
| ImageList-class | ImageList: Abstract image data list |
| image-methods | Plot an image of the pixel data of an imaging dataset |
| ImagingExperiment-class | ImagingExperiment: Abstract class for imaging experiments |
| ImagingResult-class | ImagingResult: Results of statistical analysis of imaging... |
| internal | Internal utilities for Cardinal |
| legacy | Legacy classes and methods in Cardinal |
| MassDataFrame-class | MassDataFrame: data frame with mass-to-charge ratio metadata |
| meansTest-methods | Linear model-based testing for summarized imaging experiments |
| MSContinuousImagingExperiment-class | MSContinuousImagingExperiment: "Continuous" mass spectrometry... |
| MSImagingExperiment-class | MSImagingExperiment: Mass spectrometry imaging experiments |
| MSImagingInfo-class | MSImagingInfo: Mass spectrometry imaging metadata for imzML... |
| MSProcessedImagingExperiment-class | MSProcessedImagingExperiment: "Processed" mass spectrometry... |
| mzAlign-methods | Mass align an imaging dataset |
| mzBin-methods | Mass bin an imaging dataset |
| mzFilter-methods | Filter the features of an imaging dataset by intensity |
| mz-methods | Manipulate mass-to-charge-ratio values |
| normalize-methods | Normalize an imaging dataset |
| PCA-methods | Principal components analysis |
| peakAlign-methods | Peak align an imaging dataset |
| peakBin-methods | Peak bin an imaging dataset |
| peakPick-methods | Peak pick an imaging dataset |
| pixelApply-methods | Apply functions over imaging datasets |
| plot-methods | Plot a signal from the feature data of an imaging dataset |
| PLS-methods | Partial least squares |
| PositionDataFrame-class | PositionDataFrame: data frame with spatial position metadata |
| process-methods | Delayed Processing of Imaging Datasets |
| readMSIData | Read mass spectrometry imaging data files |
| reduceBaseline-methods | Reduce the baseline for an imaging dataset |
| reexports | Objects exported from other packages |
| selectROI-methods | Select regions-of-interest of an imaging dataset |
| simulateSpectrum | Simulate a mass spectrum or MS imaging experiment |
| slice-methods | Slice an image |
| smoothSignal-methods | Smooth the signals of a imaging dataset |
| SparseImagingExperiment-class | SparseImagingExperiment: Pixel-sparse imaging experiments |
| spatialDGMM-methods | Spatially-aware Dirichlet Gaussian mixture model |
| spatialFastmap-methods | Spatially-aware FastMap projection |
| spatialKMeans-methods | Spatially-aware k-means clustering |
| spatialShrunkenCentroids-methods | Spatially-aware shrunken centroid clustering and... |
| subset-methods | Subsetting |
| topFeatures-methods | Top-ranked features from imaging analysis results |
| writeMSIData | Write mass spectrometry imaging data files |
| XDataFrame-class | XDataFrame: DataFrame with eXtra metadata columns |
