build_hmm | R Documentation |
This function builds a hidden Markov model that considers sequencing error. Uses the HMM packages.
build_hmm(num_snps, sequencing_error, avg_recomb)
num_snps |
number of SNPs, found previously from taking the number of rows in the input data. Used to set the denominator for transition probability |
sequencing_error |
User-input for expected error in sequencing (default = 0.005) |
avg_recomb |
User-input for expected average recombination spots per chromosome (default=1). Used to set the numerator for transition probability |
hmm The hidden Markov model with transition and emission probabilities set for use.
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