An R package which is a collection of the five region-based rare-variant genetic association tests. The following tests are currently implemented: ASKAT, ASKAT-Normalized, VC-C1, VC-C2 and VC-C3.
You first need to install the R package snpStats from Bioconductor:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("snpStats")You can then install the RVPedigree package from GitHub using the devtools package:
library(devtools)
devtools::install_github('GreenwoodLab/RVPedigree', build_vignettes = TRUE)Please see the included vignette to see how the functions included in this package can be used. From within R use the following command:
vignette("vignette", package = "RVPedigree")A BibTeX entry for LaTeX users:
@article{lakhal2015rare,
title={A rare variant association test in family-based designs and non-normal quantitative traits},
author={Lakhal-Chaieb, Lajmi and Oualkacha, Karim and Richards, Brent J and Greenwood, Celia MT},
journal={Statistics in medicine},
year={2015},
publisher={Wiley Online Library}
}