Robust Methods for Epistasis Detection

Functions to perform robust epistasis detection in genome-wide association studies, as described in Slim et al. (2018) . The implemented methods identify pairwise interactions between a particular target variant and the rest of the genotype, using a propensity score approach. The propensity score models the linkage disequilibrium between the target and the rest of the genotype. All methods are penalized regression approaches, which differently incorporate the propensity score to only recover the synergistic effects between the target and the genotype.


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install.packages("epiGWAS")

1.0.0 by Lotfi Slim, 2 months ago


Browse source code at https://github.com/cran/epiGWAS


Authors: Lotfi Slim [aut, cre] , Clément Chatelain [ctb] , Chloé-Agathe Azencott [ctb] , Jean-Philippe Vert [ctb]


Documentation:   PDF Manual  


GPL (>= 2) license


Imports matrixStats, DescTools, glmnet, SNPknock

Suggests foreach, iterators, precrec, parallel, doParallel, bigmemory, biglasso, testthat, knitr, rmarkdown, kableExtra


See at CRAN