getHMM: Create HMM from Parameter Values
In humburg/tileHMM: Hidden Markov Models for ChIP-on-Chip Analysis

Description Usage Arguments Value Author(s) See Also Examples

Create a two state HMM with t emission distributions from a list of parameters.

1	getHMM(params, snames)

`params`	A list with components mu, sigma and nu, each a vector with two elements. They provide values for the location parameter, scale parameter and degrees of freedom for both states. Component a is a vector of length two providing the off diagonal elements of the transition probability matrix.
`snames`	Two character strings that should be used as state names.

Object of class contHMM with the parameters provided.

Peter Humburg

hmm.setup

## create two state HMM with t distributions
state.names <- c("one","two")
transition <- c(0.035, 0.01)
location <- c(1, 2)
scale <- c(1, 1)
df <- c(4, 6)
hmm <- getHMM(list(a=transition, mu=location, sigma=scale, nu=df), 
    state.names)