viterbi              package:VanillaICE              R Documentation

_v_i_t_e_r_b_i _a_l_g_o_r_i_t_h_m

_D_e_s_c_r_i_p_t_i_o_n:

     The Viterbi algorithm for computing the most likely state sequence
     given a model

_U_s_a_g_e:

     viterbi(beta, pi, tau, states, arm, tau.scale)

_A_r_g_u_m_e_n_t_s:

    beta: emission probabilities (log scale)

      pi: initial state probabilities (log scale)

     tau: transition probabilities (log scale)

  states: character string of hidden states

     arm: character string of chromosomal arm

tau.scale: scales the probability of transitioning between an altered
          state to a normal state relative to the probability of
          transitioning between two altered states.

_D_e_t_a_i_l_s:

     The Viterbi algorithm is fit independently to each chromosomal
     arm.

     Argument 'tau.scale' is a matrix that scales the probability of
     transitioning from an altered state to a normal state to the
     probability of transitioning between two altered states.

     When initializing an object of class 'HmmParameter', the default
     is to make the probability of transitioning from an altered state
     to a normal state twice the probability of transitioning between
     two altered states. Further flexibility could be obtained by
     replacing the tau.scale matrix in an instance of the
     'HmmParameter' class with your own matrix.  The dimension of this
     matrix must be S x S, where S is the number of hidden states.

_V_a_l_u_e:

     vector of integers

_A_u_t_h_o_r(_s):

     R. Scharpf

