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.


Reference manual

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1.0.0 by Lotfi Slim, 2 months ago

Browse source code at

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