CGEN R Package

CGEN (Case-control.Genetics) is an R package for analyzing genetic data on case-control samples, with particular emphasis on novel methods for detecting Gene-Gene and Gene-Environment interactions.

• Download from Bioconductor
• License Agreement
• ReadMe
• Manual

Updates

• The new version includes snp.score function that implements a variety of score-tests for genetic association incorporating gene-environment interactions. The function, with certain options, also allows analysis of imputed SNPs.

Authors

Samsiddhi Bhattacharjee, Nilanjan Chatterjee and William Wheeler.

References

• Han SS, Rosenberg PS, Garcia-Closas M, Figueroa JD, Silverman D, Chanock SJ, Rothman N, Chatterjee N. Likelihood ratio test for detecting gene (G) environment (E) interactions under the additive risk model exploiting G-E independence for case-control data. Am J Epidemiol 2012; 176:1060-7.
• Chatterjee N, Carroll R. Semiparametric maximum likelihood estimation exploiting gene-environment independence in case-control studies (pdf). Biometrika 2005; 92:399-418.

Questions? Contact DCEG.