genomicDistance          package:VanillaICE          R Documentation

_A _r_o_u_g_h _e_s_t_i_m_a_t_e _o_f _t_h_e _g_e_n_o_m_i_c _d_i_s_t_a_n_c_e _b_e_t_w_e_e_n _S_N_P_s

_D_e_s_c_r_i_p_t_i_o_n:

     Calculates the genomic distance between SNPs as a function of the
     physical distance.  This distance is used for calculating
     transition probabilities in the viterbi algorithm.

_U_s_a_g_e:

     genomicDistance(object)
     tau(object)
     genomicDistance(object) <- value

_A_r_g_u_m_e_n_t_s:

  object: An object inheriting from 'HmmOptions'

   value: A vector of length T - 1, where T is the number of SNPs

_D_e_t_a_i_l_s:

     The genomic distance is calculated as exp(-2*d), where d is the
     physical distance in 100MB units.

     In the Viterbi algorithm, the probability of remaining in state S
     at SNP t+1 is the genomic distance.  The probability of
     transitioning to one of the alternative states is 1 - the genomic
     distance.  The 'transitionScale' function can be used to give more
     weight to transitioning back to the baseline ('normal') state.

_V_a_l_u_e:

     A numeric vector with length T-1.

_A_u_t_h_o_r(_s):

     R. Scharpf

_S_e_e _A_l_s_o:

     'transitionScale'

