Knockoffs for Hidden Markov Models and Genetic Data


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Documentation for package ‘SNPknock’ version 0.7.1

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SNPknock.fp.loadFit Load the parameter estimates obtained by fastPHASE
SNPknock.fp.loadFit_hmm Load the parameter estimates obtained by fastPHASE and assembles the HMM model for genotype data
SNPknock.fp.runFastPhase Calls fastPHASE to fit an HMM to genotype data
SNPknock.fp.writeX Convert a genetic matrix X into the fastPHASE input format
SNPknock.knockoffDMC Knockoff copies of a discrete Markov chain
SNPknock.knockoffGenotypes Knockoff copies of unphased genotypes
SNPknock.knockoffHaplotypes Knockoff copies of phased haplotypes
SNPknock.knockoffHMM Knockoff copies of a hidden Markov model
SNPknock.models.sampleDMC Sample discrete Markov chains
SNPknock.models.sampleHMM Sample hidden Markov models