Knockoffs for Hidden Markov Models and Genetic Data

Generate knockoffs for genetic data and hidden Markov models. For more information, see the website below and the accompanying papers: "Gene hunting with hidden Markov model knockoffs", Sesia et al., Biometrika, 2019, (). "Multi-resolution localization of causal variants across the genome", Sesia et al., bioRxiv, 2019, ().


SNPknock 0.5.0 (10/10/2017)

Initial release

SNPknock 0.5.1 (09/01/2018)

Added a new vignette describing the usage of SNPknock with genotype data.

SNPknock 0.6.0 (02/04/2018)

Changed the functions loading parameter estimates produced by fastPhase. Using "_origchar" file instead of first row of X. Added support for haplotype HMM. Using integer storage for X.

SNPknock 0.7.0 (05/24/2018)

Improved memory efficiency and added support for multithreading. Added more efficient functions for generating knockoff copies of unphased genotypes and phased haplotypes.

SNPknock 0.7.1 (05/30/2018)

Fixed bug in the generation of knockoff copies for unphased genotypes and phased haplotypes.

Reference manual

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0.8.2 by Matteo Sesia, 5 days ago

Report a bug at

Browse source code at

Authors: Matteo Sesia [aut, cre]

Documentation:   PDF Manual  

GPL-3 license

Imports Rcpp, Rdpack

Suggests knitr, testthat, parallel, doParallel

Linking to Rcpp, RcppArmadillo, RcppProgress

Imported by epiGWAS.

See at CRAN