SMAPHMM-class: Class "SMAPHMM": A class to manage HMMs for the SMAP package
Description
Holds parameters for a Hidden Markov Model (HMM) used in
the SMAP package.Objects from the Class
Objects should not be created directly but via the
constructor function SMAPHMM.Slots
A:- Object of class
"matrix" The transition
probability matrix between states. Pi:- Object of class
"numeric" The initial
probabilities of starting in a certain state. Phi:- Object of class
"matrix" A matrix that
specifies the paramaters of Gaussian distributions associated with
each hidden state. The first column specifies standard deviations,
the second specifies means. noStates:- Object of class
"numeric" The number
of hidden states in the HMM. Z:- Object of class
"matrix" Matrix of
transition probabilities. Y:- Object of class
"numeric" Vector of
initial probabilities. eta:- Object of class
"ANY". Internal slot. grad:- Object of class
"ANY". Internal slot.
Methods
- A
signature(object = "SMAPHMM"): Returns the
transition matrix.- Pi
signature(object = "SMAPHMM"): Returns the initial
probabilities.- Phi
signature(object = "SMAPHMM"): Returns the
distribution parameter matrix.- noStates
signature(object = "SMAPHMM"): Returns the
number of hidden states in the HMM.
References
Andersson, R., Bruder, C. E. G., Piotrowski, A., Menzel, U., Nord, H.,
Sandgren, J., Hvidsten, T. R., Diaz de Stahl, T., Dumanski, J. P.,
Komorowski, J., A Segmental Maximum A Posteriori Approach to Array-CGH
Copy Number Profiling, submitted