Learn R Programming
signalHsmm (version 1.3)

add_k_mer_state: 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,}
  • tpmpara matrix with new transition probabilities between states,
  • odmatrix of new response probabilities,
  • paramsmatrix of new probability distributions for duration.