Description Usage Arguments Value Note
Changes parameters for Hidden SemiMarkov Model to add kmer
1  add_k_mer_state(kMer, pipar, tpmpar, od, params, pState, nState, pTrans, d)

kMer 

pipar 
Probabilities of initial state in Markov Model. 
tpmpar 
Matrix with transition probabilities between states. 
od 
Matrix of response probabilities. Eg. od[1,2] is a probability of signal 2 in state 1. 
params 
Matrix of probability distribution for duration. Eg. params[10,2] is probability of duration of time 10 in state 2. 
pState 
number denoting hidden state right before kmer. 
nState 
number denoting hidden state right after kmer. 
pTrans 
Probability of change from pState to kmer hidden state. 
d 
Duration of the state. 
A list of length four:
pipar a vector of new probabilities of initial state in Markov Model,
tpmpar a matrix with new transition probabilities between states,
od matrix of new response probabilities,
params matrix of new probability distributions for duration.
Currently add only kmers without distance.
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