calculateDistance         package:VanillaICE         R Documentation

_C_a_l_c_u_l_a_t_e_s _t_h_e _p_h_y_s_i_c_a_l _d_i_s_t_a_n_c_e _b_e_t_w_e_e_n _a_d_j_a_c_e_n_t _S_N_P_s

_D_e_s_c_r_i_p_t_i_o_n:

     Calculates the distance between adjacent SNPs.

_U_s_a_g_e:

     calculateDistance(object)
     physicalDistance(object)

_A_r_g_u_m_e_n_t_s:

  object: Object inheriting from 'SnpLevelSet'

_D_e_t_a_i_l_s:

     Calculates the physical distance between adjacent SNPs along a
     chromosome.

_V_a_l_u_e:

     A vector of integers

_N_o_t_e:

     The transition probabilities in the Viterbi algorithm are
     calculated as a function of the physical distance (d) between
     adjacent SNPs.

     probability of staying in state S = exp(-2 * d/100*1e6)

_A_u_t_h_o_r(_s):

     R. Scharpf

_S_e_e _A_l_s_o:

     'viterbi'

