SMAP (version 1.36.0)

SMAPHMM: Constructor for "SMAPHMM" objects

Description

A constructor for SMAPHMM-class objects.

Usage

SMAPHMM(noStates, Phi, A=NULL, Pi=rep(1/noStates,noStates), initTrans=0.2/(noStates - 1))

Arguments

noStates

The number of hidden states in the HMM (numeric).

Phi

A Gaussian distribution parameter matrix (numeric).

A

A noStates * noStates matrix of transition probabilities betweeen the hidden states (numeric).

Pi

A vector of initial probabilities of starting in a certain state (numeric).

initTrans

Specifies the transition probability between non-equal states (numeric).

Value

An object of class SMAPHMM-class.

Details

Phi is a noStates * 2 matrix that specifies the paramaters of Gaussian distributions associated with each hidden state. The first column specifies standard deviations, the second specifies means.

If A == NULL, initTrans specifies the transition probability between states i and j in 1:noStates, such that i != j. Only used if A == NULL. initTrans * noStates must be smaller than (or equal to) 1.

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-class, SMAPObservations-class