RRIntCC: Region-Region Interaction Detection in Genome-Wide Association Case-Control Studies

About RRIntCC

In genome-wide association study (GWAS), conventional interaction detection methods like BOOST are mostly based on SNP-SNP interactions. Although single nucleotides are the building blocks of human genome, single nucleotide polymorphisms (SNPs) are not necessarily the smallest functional unit for complex phenotypes. Region-based strategies have been proved to be successful in studies aiming at marginal effects. In this paper, we developed RRIntCC, a novel region-region interaction detection method for case-control studies, by utilizing the correlations between individual SNP-SNP interactions based on linkage disequilibrium (LD) contrast test.


Where to download RRIntCC

The source code is available at:
RRIntCC:   RRIntCC.zip


Environment configuration

Install R, Rcpp and RInside dependencies:

1. Need to install R base env: sudo apt install r-base-core
2. Need to install mvtnorm, Rcpp and RInside (The packages can be downloaded online): sudo R CMD INSTALL xxx.tar.gz


How to use it?

Please read rrintcc_read.me in the zip file for details.
For any enquiry, please contact ZHANG Sen at szhangat@connect.ust.hk