Skip to content
This repository has been archived by the owner on Oct 12, 2023. It is now read-only.

molpopgen/buRden

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

#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".

About

Rcpp functions for performing "burden" tests.

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published