InitialAlignment       package:GraphAlignment       R Documentation

_C_r_e_a_t_e _i_n_i_t_i_a_l _a_l_i_g_n_m_e_n_t

_D_e_s_c_r_i_p_t_i_o_n:

     Create a permutation for an initial alignment. Either "random" or
     "reciprocal" may be specified as the mode argument.

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

     InitialAlignment(psize, r=NA, mode="random")

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

   psize: size of the alignment

       r: node similarity score matrix (required for mode 'reciprocal')

    mode: type of initial alignment

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

     To create a random initial alignment of size psize, the
     InitialAlignment function can be used with the mode argument set
     to "random". If mode is set to "reciprocal", a reciprocal best
     match algorithm is applied to the input matrix R to find an
     initial alignment. This mode requires that the psize argument is
     sufficiently large to allow for the addition of dummy nodes to
     which unaligned nodes can formally be aligned.

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

     The return value is a permutation vector of the specified size.

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

     Joern P. Meier, Michal Kolar, Ville Mustonen, Michael Laessig, and
     Johannes Berg

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

       ex<-GenerateExample(dimA=22, dimB=22, filling=.5, covariance=.6,
         symmetric=TRUE, numOrths=10, correlated=seq(1,18))
       
       pinitial<-InitialAlignment(psize=34, r=ex$r, mode="reciprocal")

