wtest: an integrated R package for genetic epistasis testing

Abstract

Abstract Background With the increasing amount of high-throughput genomic sequencing data, there is a growing demand for a robust and flexible tool to perform interaction analysis. The identification of SNP-SNP, SNP-CpG, and higher order interactions helps explain the genetic etiology of human diseases, yet genome-wide analysis for interactions has been very challenging, due to the computational burden and a lack of statistical power in most datasets. Results The wtest R package performs association testing for main effects, pairwise and high order interactions in genome-wide association study data, and cis-regulation of SNP and CpG sites in genome-wide and epigenome-wide data. The software includes a number of post-test diagnostic and analysis functions and offers an integrated toolset for genetic epistasis testing. Conclusions The wtest is an efficient and powerful statistical tool for integrated genetic epistasis testing. The package is available in CRAN: https://CRAN.R-project.org/package=wtest.

Keywords

• Epistasis testing
• Association study
• R package