ComputeScores         package:GraphAlignment         R Documentation

_C_o_m_p_u_t_e _s_c_o_r_e_s

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

     Compute scores.

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

     ComputeScores(A, B, R, P, linkScore, selfLinkScore, nodeScore1,
       nodeScore0, lookupLink, lookupNode, symmetric=TRUE, clamp=TRUE)

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

       A: adjacency matrix for network A

       B: adjacency matrix for network B

       R: node similarity matrix

       P: permutation vector to be used as the initial alignment (see
          InitialAlignment)

linkScore: link score matrix (see ComputeLinkParameters)

selfLinkScore: self link score matrix (see ComputeLinkParameters)

nodeScore1: node score vector (s1) (see ComputeNodeParameters)

nodeScore0: node score vector for unaligned nodes (s0) (see
          ComputeNodeParameters)

lookupLink: link bin lookup table (see GetBinNumber)

lookupNode: node bin lookup table (see GetBinNumber)

symmetric: network symmetry flag

   clamp: clamp values to range when performing bin lookups

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

     This function computes log-likelihood scores for an alignment
     using the specified scoring tables, two networks A and B and their
     alignment P. The total score of the alignment has two
     contributions, the first coming from the sequence homology (node
     similarity, sn) and the second from the similarity of interaction
     networks (sl).

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

     The return value is a list containing the link score (sl) and the
     node score (sn).

_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)
       
       lookupNode<-c(-.5,.5,1.5)
       nodeParams<-ComputeNodeParameters(dimA=22, dimB=22, ex$r,
         pinitial, lookupNode)
       
       al<-AlignNetworks(A=ex$a, B=ex$b, R=ex$r, P=pinitial,
         linkScore=linkParams$ls,
         selfLinkScore=linkParams$ls,
         nodeScore1=nodeParams$s1, nodeScore0=nodeParams$s0,
         lookupLink=lookupLink, lookupNode=lookupNode,
         bStart=.1, bEnd=30,
         maxNumSteps=50)
       
       ComputeScores(A=ex$a, B=ex$b, R=ex$r, P=al,
         linkScore=linkParams$ls,
         selfLinkScore=linkParams$ls,
         nodeScore1=nodeParams$s1, nodeScore0=nodeParams$s0,
         lookupLink=lookupLink, lookupNode=lookupNode,
         symmetric=TRUE)

