Plot transition probabilities

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Description

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

Usage

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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 M. Rueda and Ramon Diaz-Uriarte

References

Rueda OM, Diaz-Uriarte R. Flexible and Accurate Detection of Genomic Copy-Number Changes from aCGH. PLoS Comput Biol. 2007;3(6):e122

Examples

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## 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)
plotQNH(x=x, beta=beta, q=-beta, col=c(1,2))