Man pages for SNPknock
Knockoffs for Hidden Markov Models and Genetic Data
| assemble_pEmit | Compute the genotype emission distributions based on the... |
| assemble_pEmit_phased | Compute the haplotype emission distributions based on the... |
| assemble_pInit | Compute the genotype initial distributions based on the... |
| assemble_pInit_phased | Compute the haplotype initial distributions based on the... |
| assemble_Q | Compute the genotype transition matrices based on the... |
| compute_Q1 | Compute the haplotype transition matrices based on the... |
| GroupGenotypes_wrapper | Wrapper for GroupGenotypes |
| GroupHaplotypes_wrapper | Wrapper for GroupHaplotypes |
| knockoffDMC | Group knockoffs of discrete Markov chains |
| knockoffDMC_wrapper | Wrapper for DMC group knockoffs |
| knockoffGenotypes | Group-knockoffs of unphased genotypes |
| knockoffHaplotypes | Group-knockoffs of phased haplotypes |
| knockoffHMM | Group knockoffs of hidden Markov models |
| knockoffHMM_wrapper | Wrapper for HMM group knockoffs |
| loadEMParameters | Read the files produced by fastPHASE |
| loadHMM | Load HMM parameters fitted by fastPHASE |
| rand_weighted | Random sampling from discrete distribution |
| runFastPhase | Fit an HMM to genetic data using fastPHASE |
| sampleDMC | Sample discrete Markov chains |
| sampleHMM | Sample hidden Markov models |
| writeXtoInp | Convert genotypes X into the fastPHASE input format |
