ComputeLinkParameters     package:GraphAlignment     R Documentation

_C_o_m_p_u_t_e _l_i_n_k _p_a_r_a_m_e_t_e_r_s

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

     Compute the optimal scoring parameters (link score) for a given
     alignment.

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

     ComputeLinkParameters(A, B, P, lookupLink, clamp=TRUE)

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

       A: adjacency matrix for network A

       B: adjacency matrix for network B

       P: permutation vector (see InitialAlignment, AlignNetworks)

lookupLink: link bin lookup table (see GetBinNumber)

   clamp: clamp values to range when performing bin lookups

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

     This function computes optimal link score parameters for use with
     ComputeM and AlignNetworks. It takes two matrices as well as an
     initial alignment P and the lookup table for link binning,
     lookupLink, as parameters.

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

     The return value is a list containing the self link score matrix
     (lsSelf) and the link score matrix (ls).

_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")
       
       lookupLink<-seq(-2,2,.5)
       linkParams<-ComputeLinkParameters(ex$a, ex$b, pinitial, lookupLink)

