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(initialStateProbs, emission, tau, arm, tau.scale, verbose =
     FALSE, chromosome, position, sampleNames, locusNames, normalIndex, returnLikelihood = FALSE)

_A_r_g_u_m_e_n_t_s:

initialStateProbs: initial state probabilities (log scale)

emission: matrix of log emission probabilities (one sample is a matrix)

     tau: transition probabilities (original scale)

     arm: numeric or character string indicating chromosomal arm

tau.scale: matrix to scale the probability of transitioning between
          states.

 verbose: Logical

chromosome: chromosome

position: physical position

sampleNames: sample labels

locusNames: labels for loci

normalIndex: index corresponding to the normal state. See details

returnLikelihood: whether to return the 'loglikelihood'

_D_e_t_a_i_l_s:

     The Viterbi algorithm is fit independently to each chromosomal arm
     if arm is specified.

     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.  If
     missing, tau.scale is 1 (no scaling)

_V_a_l_u_e:

  matrix: predicted states

_A_u_t_h_o_r(_s):

     R. Scharpf

