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Generates knockoffs of HMMs and genetic data.

Project description

SNPknock is a simple Python package for creating knockoffs of hidden Markov models and genetic data.

This package implements the algorithms described in the following papers:

Feature highlights:

  • Generate knockoffs for discrete Markov chains (DMC).
  • Generate knockoffs for hidden Markov models (HMM).
  • Generate knockoffs for genotype and haplotype data.
  • Provides a user-friendly interface for fitting an HMM to genetic data using the software fastPhase.

If you want to learn about applying SNPknock to analyze data from large genome-wide association studies, see KnockoffZoom: https://msesia.github.io/knockoffzoom

Released under the GPL-v3 license - see the file LICENSE in the source distribution.

Project details


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Files for SNPknock, version 0.8.3
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