Cardinal provides an interface for manipulating mass spectrometry (MS) imaging datasets, simplifying most of the basic programmatic tasks encountered during the statistical analysis of MS 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.
Cardinal can be installed via the BiocManager package.
This is the recommended installation method.
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Cardinal")The same function can be used to update Cardinal and other Bioconductor packages.
Once installed, Cardinal can be loaded with library():
library(Cardinal)Cardinal can also be installed via the remotes package.
if (!require("remotes", quietly = TRUE))
install.packages("remotes")
remotes::install_github("kuwisdelu/Cardinal", ref=remotes::github_release())Previous releases can be installed by specifying the exact version.
remotes::install_github("kuwisdelu/Cardinal@v3.6.2")The Bioconductor development version of Cardinal can also be installed via the BiocManager package.
BiocManager::install("Cardinal", version="devel")This version is unstable and should not be used for critical work. However, it is typically more stable than Github devel.
This version should typically pass R CMD check without errors.
The most cutting edge version of Cardinal can be installed from Github via the remotes package.
if (!require("remotes", quietly = TRUE))
install.packages("remotes")
remotes::install_github("kuwisdelu/Cardinal")This version is unstable and only recommended for developers. It should not be used for critical work.