/buRden

Rcpp functions for performing "burden" tests.

Primary LanguageC++BSD 2-Clause "Simplified" LicenseBSD-2-Clause

#Association test software from the Thornton Lab

##Obtaining the source

git clone https://github.com/molpopgen/buRden

##Dependencies

  1. R v3.1.0 or greater
  2. Rcpp v0.11.1 or greater
  3. The boost C++ libraries

The package has been tested with various version of GCC (all versions 4.6.4 or greater) and clang (version clang-503.0.38) on OS X Mavericks.

##Installation

The most straightforward approach is via R's devtools package:

library(devtools)
install_github("molpopgen/buRden")

The package may also be installed the "traditional" way:

R CMD INSTALL buRden

To install into a custom location:

R_LIBS=/path/to/special/place R CMD INSTALL buRden

Or, using the devtools approach, invoke R:

R_LIBS=/path/to/special/place R

And then, from the R shell:

library(devtools)
install_github("molpopgen/buRden")

##Documentation

All documentation is provided via R's help system. You may build the pdf of the package manual using the following command:

R CMD Rd2pdf buRden

##Tests implemented:

  1. Madsen and Browning (2009)
  2. C-alpha
  3. ESM
  4. A chi-squared test of the null model that the proportions of cases and controls carrying rare variants are the same. This is equivalent to Li and Leal's "collapsing method".