A Bioconductor package for meta analysis of high-throughput datasets using enriched feature annotations instead of just the features themselves.
Note that this is a rewrite of the categoryCompare package. For more information about how things have changed and why, please see this poster.
API
This version is mostly complete and works for many full analyses. The user facing API is expected to be close to fixed, especially for the core functionality. Some methods need actual S4 or R6 based objects and methods, but we expect that the function calls themselves will remain the same.
To Do
Things that are still needed include:
- Wrapper for initial analysis when given feature data and annotations
- Example for importing the users own annotations
- Integration of
GOCatsPython library for summarizing ontologies - Better exploration of features that are linked to specific annotations, including the original data associated with the features
Documentation
The Vignette provides a description of the thinking behind this package as well as a toy example for demonstration purposes.
Installation
Installation of this package from Github requires the remotes package.
install.packages("remotes")
library(remotes)
install_github("MoseleyBioinformaticsLab/categoryCompare2")Mac Installation
There is one issue with installation on MacOS, and that is the {Cairo} package. This is actually due to having to have xquartz installed. The easiest way I can find to install it is using homebrew. In a terminal, you can do:
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
brew install --cask xquartz
R
install.packages("Cairo") # skip if already installed
library(Cairo)Hopefully that worked fine, and now you should be able to use all the functionality in {categoryCompare2}.
Citation
Flight RM, Harrison BJ, Mohammad F, Bunge MB, Moon LDF, Petruska JC and Rouchka EC (2014). .CATEGORYCOMPARE, an analytical tool based on feature annotations. Frontiers in Genetics. link