wtest: an integrated R package for genetic epistasis testing.
Authors of this article are:
Sun R, Xia X, Chong KC, Zee BC, Wu WKK, Wang MH.
A summary of the article is shown below:
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.
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This article is a good source of information and a good way to become familiar with topics such as: Association study; Epistasis testing; R package.
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