Cardinal-package {Cardinal} | R Documentation

## Mass spectrometry imaging tools

### Description

Implements statistical & computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification.

### Details

Cardinal provides an abstracted interface to manipulating mass spectrometry imaging datasets, simplifying most of the basic programmatic tasks encountered during the statistical analysis of imaging data. These include image manipulation and processing of both images and mass spectra, and dynamic plotting of both.

While pre-processing steps including normalization, baseline correction, and peak-picking are provided, the core functionality of the package is statistical analysis. The package includes classification and clustering methods based on nearest shrunken centroids, as well as traditional tools like PCA and PLS.

Type `browseVignettes("Cardinal")` to view a user's guide and vignettes of common workflows.

### Options

The following options can be set via `options()`.

- `options(Cardinal.verbose=interactive())`: Should detailed messages be printed?

- `options(Cardinal.progress=interactive())`: Should a progress bar be shown?

- `options(Cardinal.numblocks=20)`: The default number of data chunks used by `pixelApply()`, `featureApply()`, and `spatialApply()` when `.blocks=TRUE`. Used by many methods internally.

- `options(Cardinal.delay=TRUE)`: Should pre-processing functions like `normalize()` and `peakPeak()` be delayed (until `process()` is called)?

- `options(Cardinal.dark=FALSE)`: Should the default theme for new plots use dark mode?

### Author(s)

Kylie A. Bemis

Maintainer: Kylie A. Bemis <k.bemis@northeastern.edu>

[Package Cardinal version 2.4.0 Index]