hmm: Create an rphast HMM object

In rphast: Interface to 'PHAST' Software for Comparative Genomics

Description

Create a new HMM object

Usage

hmm(trans.mat, eq.freq = NULL, begin.freq = NULL, end.freq = NULL)

Arguments

trans.mat	A square matrix object of dimension n x n where n is the number of states, and element [i,j] is the rate of transition from state i to state j
eq.freq	A vector of length n giving the equilibrium frequencies of each state. If NULL, calculate equilibrium frequencies that will make a reversible markov chain.
begin.freq	A vector of length n giving the initial state frequencies. If NULL, use equilibrium frequencies.
end.freq	A vector of length n giving the final state frequencies. If NULL, do not condition on end frequencies.

Author(s)

Melissa J. Hubisz and Adam Siepel

Examples

h <- hmm(matrix(1, nrow=4, ncol=4))
h

rphast documentation built on May 1, 2019, 9:26 p.m.