Knockoffs for Hidden Markov Models and Genetic Data

Generates knockoff variables from discrete Markov chains and hidden Markov models, with specific support for genetic data. For more information, see the website below and the accompanying paper: Sesia et al., "Gene Hunting with Knockoffs for Hidden Markov Models", 2017, .


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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0.7.1 by Matteo Sesia, 10 months ago

Browse source code at

Authors: Matteo Sesia

Documentation:   PDF Manual  

GPL (>= 2) license

Imports Rcpp

Suggests knitr, testthat, parallel, doParallel

Linking to Rcpp, RcppProgress

Imported by epiGWAS.

See at CRAN