plot.Q.NH {RJaCGH} | R Documentation |
Plot the probabilities of staying in the same state for a non-homogenous hidden Markov model.
plot.Q.NH(x, beta, q=-beta, col = NULL, ...)
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 |
Please note that RJaCGH model imposes that q
is -beta
, and
distances are normalized to lay between 0 and 1.
A plot is produced showing the probability of staying in the same hidden state versus distance between adjacent genes, for every state.
Oscar M. Rueda and Ramon Diaz-Uriarte
Rueda OM, Diaz-Uriarte R. Flexible and Accurate Detection of Genomic Copy-Number Changes from aCGH. PLoS Comput Biol. 2007;3(6):e122
## 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))