wtest: an integrated R package for genetic epistasis testing

Abstract

BackgroundWith 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.ResultsThe 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.ConclusionsThe 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.

Immune System and Neuroinflammation in Idiopathic Parkinson’s Disease: Association Analysis of Genetic Variants and miRNAs Interactions

“…Genetic epistasis testing was performed among significant SNPs from Fisher’s exact test using W -test, which measures the association between binary phenotype and categorical genetic data ( Sun et al, 2019 ). Obtained p were adjusted by means of Bonferroni correction with threshold set at p < 0.01 and number of categorical combination ( k > 6) based on visual inspection of diagnostic plots ( Sun et al, 2019 ).…”

Evaluating the detection ability of a range of epistasis detection methods on simulated data for pure and impure epistatic models

“…For example, Cassi and PLINK encompass a Z-score based test, termed fast-epistasis, while adopting slightly differing logistic regression approaches, with PLINK also implementing the Wan Log-Linear method, BOOST [17][18][19]. Another, more recent example is the wtest R package, that uses a novel statistic approach to compare distributional differences present in the alleles of cases and controls, using a χ 2 distribution [20].…”

Genetic Determinants Highlight the Existence of Shared Etiopathogenetic Mechanisms Characterizing Age-Related Macular Degeneration and Neurodegenerative Disorders

“…Results were visualized by generating a heatmap matrix. Genetic epistasis testing was performed among significant SNPs from Fisher's exact test using W-test, which can measure the association between binary phenotype and categorical genetic data (26). Only the main effects and pairwise variant interactions were tested.…”

“…Only the main effects and pairwise variant interactions were tested. The obtained p-values were adjusted by means of Bonferroni correction set at p < 0.0005 and number of categorical combinations (k ≥ 8) (26).…”