Knockoffs for Hidden Markov Models and Genetic Data
Compute the genotype emission distributions based on the fastPHASE HMM
Compute the haplotype emission distributions based on the fastPHASE HM...
Compute the genotype initial distributions based on the fastPHASE HMM
Compute the haplotype initial distributions based on the fastPHASE HMM
Compute the genotype transition matrices based on the fastPHASE HMM
Compute the haplotype transition matrices based on the fastPHASE HMM
Wrapper for GroupGenotypes
Wrapper for GroupHaplotypes
Group knockoffs of discrete Markov chains
Wrapper for DMC group knockoffs
Group-knockoffs of unphased genotypes
Group-knockoffs of phased haplotypes
Group knockoffs of hidden Markov models
Wrapper for HMM group knockoffs
Read the files produced by fastPHASE
Load HMM parameters fitted by fastPHASE
Random sampling from discrete distribution
Fit an HMM to genetic data using fastPHASE
Sample discrete Markov chains
Sample hidden Markov models
Convert genotypes X into the fastPHASE input format
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, (<doi:10.1093/biomet/asy033>). "Multi-resolution localization of causal variants across the genome", Sesia et al., bioRxiv, 2019, (<doi:10.1101/631390>).