add_k_mer_state: Adds k-mer hidden state to signalHsmm model

Description Usage Arguments Value Note

View source: R/add_k_mer_state.R

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.



signalHsmm documentation built on May 19, 2017, 11:04 p.m.
Search within the signalHsmm package
Search all R packages, documentation and source code

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.