burdenBalanceR is a package to streamline interpretable genetic variant burden testing, inspired by use cases in pediatric leukemia and immune disorders. We support Aeon output with updated allele frequencies from gnomAD. We are adding local ancestry inference support for FLARE and Recomb-Mix, and variant signature discovery (germline, somatic, or joint) is supported via RcppML 1.0. Traditional kernel-based association testing with SKAT is in process for comparison purposes.
The overarching goal of burdenBalanceR is as the name states -- to balance the cognitive load involved in addressing population stratification and bias against a desire for fast, accurate estimates of rare variant burdens in rare diseases. As previously noted, the perfect is the enemy of the good, and you can cite us (or Blaise Pascal) on that.
The pre-release version of the package can be pulled from GitHub:
if (!require("BiocManager")) install.packages("BiocManager")
BiocManager::install("trichelab/burdenBalanceR", build_vignettes=TRUE)
The repository includes a Makefile to facilitate some common tasks.
$ make test. Requires the testthat package. You can also specify a specific test file or files to run by adding a "file=" argument, like $ make test file=logging. test_package will do a regular-expression pattern match within the file names. See its documentation in the testthat package.
$ make doc. Requires the roxygen2 package.