SMAPHMM-class {SMAP}R Documentation

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 are not intended to 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.

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.

Author(s)

Robin Andersson, robin.andersson@lcb.uu.se

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

See Also

smap, SMAPHMM


[Package SMAP version 1.4.0 Index]