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 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.

### 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 1.56.0 Index]