plot.Q.NH {RJaCGH}R Documentation

Plot transition probabilities

Description

Plot the probabilities of staying in the same state for a non-homogenous hidden Markov model.

Usage

plot.Q.NH(x, beta, q=-beta, col = NULL, ...)

Arguments

x Vector of distances between observations
beta beta parameter of the transition matrix. Must be a square matrix with the same size as the number of hidden states
q q parameter of the transition matrix. Must be a square matrix with the same size as the number of hidden states
col vector of colors for each state. Must be of the same size as the number of hidden states
... aditional arguments passed to plot

Details

Please note that RJaCGH model imposes that q is -beta, and distances are normalized to lay between 0 and 1.

Value

A plot is produced showing the probability of staying in the same hidden state versus distance between adjacent genes, for every state.

Author(s)

Oscar Rueda and Ramon Diaz-Uriarte

References

Oscar Rueda and Ramon Diaz Uriarte, in prep.

Examples

## Model with two hidden states
## Note that RJaCGH normalizes distances to be between 0 and 1
x <- rexp(99)
x <- x/ max(x)
beta <- matrix(c(0, 1, 3, 0), 2, 2)
plot.Q.NH(x=x, beta=beta, q=-beta, col=c(1,2))

[Package RJaCGH version 0.4 Index]