HmmParameter-class        package:VanillaICE        R Documentation

_C_l_a_s_s "_H_m_m_P_a_r_a_m_e_t_e_r"

_D_e_s_c_r_i_p_t_i_o_n:

     Parameters needed for the Viterbi algorithm, including emission
     probabilities, the genomic distance, and the initial state
     probabilities

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new("HmmParameter",
     states, initialStateProbability, emission, genomicDistance,
     transitionScale)'.

_S_l_o_t_s:


     '_s_t_a_t_e_s': Object of class '"character"' 

     '_i_n_i_t_i_a_l_S_t_a_t_e_P_r_o_b_a_b_i_l_i_t_y': Object of class '"numeric"' 

     '_e_m_i_s_s_i_o_n': Object of class '"array"' 

     '_g_e_n_o_m_i_c_D_i_s_t_a_n_c_e': Object of class '"numeric"' 

     '_t_r_a_n_s_i_t_i_o_n_S_c_a_l_e': Object of class '"matrix"' 

_M_e_t_h_o_d_s:


     [ 'signature(x = "HmmParameter")':  

     _e_m_i_s_s_i_o_n 'signature(object = "HmmParameter")':  

     _e_m_i_s_s_i_o_n<- 'signature(object = "HmmParameter", value = "array")':  

     _g_e_n_o_m_i_c_D_i_s_t_a_n_c_e 'signature(object = "HmmParameter")':  

     _g_e_n_o_m_i_c_D_i_s_t_a_n_c_e<- 'signature(object = "HmmParameter", value =
          "numeric")':  

     _h_m_m 'signature(object = "HmmOptions", params = "HmmParameter")':  

     _i_n_i_t_i_a_l_i_z_e 'signature(.Object = "HmmParameter")':  

     _p_i 'signature(object = "HmmParameter")':  

     _s_h_o_w 'signature(object = "HmmParameter")':  

     _s_t_a_t_e_s 'signature(object = "HmmParameter")':  

     _s_t_a_t_e_s<- 'signature(object = "HmmParameter", value =
          "character")':  

     _t_a_u 'signature(object = "HmmParameter")':  

     _t_r_a_n_s_i_t_i_o_n_S_c_a_l_e 'signature(object = "HmmParameter")':  

     _t_r_a_n_s_i_t_i_o_n_S_c_a_l_e<- 'signature(object = "HmmParameter", value =
          "matrix")':  

_N_o_t_e:

     See HmmParameter vignette

_A_u_t_h_o_r(_s):

     RS

_S_e_e _A_l_s_o:

     'HmmOptions-class'

_E_x_a_m_p_l_e_s:

     showClass("HmmParameter")

