add_k_mer_state {signalHsmm}

Adds k-mer hidden state to signalHsmm model

Description

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

Usage

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.