SMAPHMM                 package:SMAP                 R Documentation

_C_o_n_s_t_r_u_c_t_o_r _f_o_r "_S_M_A_P_H_M_M" _o_b_j_e_c_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     A constructor for 'SMAPHMM-class' objects.

_U_s_a_g_e:

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

_A_r_g_u_m_e_n_t_s:

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).

_D_e_t_a_i_l_s:

     '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.

_V_a_l_u_e:

     An object of class 'SMAPHMM-class'.

_A_u_t_h_o_r(_s):

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

_R_e_f_e_r_e_n_c_e_s:

     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

_S_e_e _A_l_s_o:

     'smap', 'SMAPHMM-class', 'SMAPObservations-class'

