Adds k-mer hidden state to signalHsmm model

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Description

Changes parameters for Hidden Semi-Markov Model to add k-mer

Usage

1
add_k_mer_state(kMer, pipar, tpmpar, od, params, pState, nState, pTrans, d)

Arguments

kMer

character vector representing k-mer aminoacid sequence.

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 k-mer.

nState

number denoting hidden state right after k-mer.

pTrans

Probability of change from pState to k-mer hidden state.

d

Duration of the state.

Value

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.

Note

Currently add only k-mers without distance.