10X Genomics Cell Ranger R kit
Description
R package that accompanies the 10X Genomics Cell Ranger pipeline. It supports manipulation and visualization of output from the pipeline as well as re-running of secondary analyses.
Development
Make sure you have R packages devtools and roxygen2 installed and loaded:
install.packages( c('devtools', 'roxygen2') )
library(devtools)
library(roxygen2)To install the current version from master:
install_github( '10XDev/cellrangerRkit', user = 'github_user',
auth_token = 'some_auth_token' )The auth token can be generated using the default settings in https://github.com/settings/applications under 'Personal access tokens'. Make sure to save the token, otherwise you need to generate another one.
Workflow
Since you've already installed devtools, you should consider using it to help
develop the package. Note that all 'path/to/working/copy' strings can be
replaced by the empty string if you're inside the root of the package directory
(which I strongly recommend). There is a developer mode you can enter by
typing:
dev_mode()and exit similarly. What this does is create a sandboxed development environment for your packages.
Throughout development, you probably will need to load updates regularly:
install('path/to/working/copy')If you're trying to access a new function outside of the package (in
userspace land) make sure to add the @export decorator and generate
documentation for it using roxygen2:
document('path/to/working/copy')Once you dig the changes and you think it's stable, drop out of developer mode and install it into your main package set.
Testing
We are using the testthat package for unit testing. All tests live in
inst/tests/. The directory tests/ simply contains a stub to test all things
that live in inst/tests/.
To run all tests, in Rstudio go to: Build.. Test Package
Using devtools you can call all tests by running:
test('path/to/working/copy')Building for distribution
make rkit && R CMD INSTALL . && make vignette
Uninstalling
remove.packages('cellrangerRkit')