scaleTransitionProbability    package:VanillaICE    R Documentation

_S_c_a_l_e_s _t_h_e _p_r_o_b_a_b_i_l_i_t_y _o_f _t_r_a_n_s_i_t_i_o_n_i_n_g _b_e_t_w_e_e_n _t_w_o _s_t_a_t_e_s _i_n _t_h_e
_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:

     Scales the probability of transitioning between two states in the
     Viterbi algorith

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

     scaleTransitionProbability(object, SCALE = 2, normalLabel = "N")

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

  object: Object of class 'HmmOptions'

   SCALE: Numeric. See details.

normalLabel: Character: label used for the baseline state.

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

     If SCALE is 2, the probability of transitioning from an altered
     state back to the normal state is twice the probability of
     transition from an altered state to another altered state.

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

     A matrix of dimension S x S, where S is the number of states.  The
     diagonal should always be 1 (we do not scale the probability of
     remaining in the same state).  A slot for storing this matrix is
     provided in the 'HmmParameter' class.

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

     RS

_S_e_e _A_l_s_o:

     'genomicDistance', 'transitionScale', 'HmmParameter-class'

_E_x_a_m_p_l_e_s:

     data(chromosome1)
     options <- new("HmmOptions",
                    states=c("D", "N", "L", "A"),
                    snpset=chromosome1,
                    copyNumber.location=c(1, 2, 2, 3),
                    probHomCall=c(0.99, 0.7, 0.99, 0.7))
     scaleTransitionProbability(options)

