AnalyzeAlignment       package:GraphAlignment       R Documentation

_A_n_a_l_y_z_e _a_n _a_l_i_g_n_m_e_n_t

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

     Analyze an alignment between two networks.

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

     AnalyzeAlignment(A, B, R, P, lookupNode, epsilon, clamp)

_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

lookupNode: node bin lookup vector

 epsilon: node similarity threshold

   clamp: clamp values to range when performing bin lookups

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

     This function analyzes an alignment and returns various
     characteristics.

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

     The return value is a list containing the results. Defined values
     are:

     na - number of aligned node pairs

     nb - number of aligned node pairs where neither partner has
     appreciable sequence similarity with any node in the other
     network. Appreciable sequence similarity means that r>epsilon.
     Formally, this is the number of aligned node pairs (ia, ib), where
     no jb exists such that R[ia, jb] > epsilon and no ja such that
     R[ja, ib] > epsilon.

     nc - number of aligned node pairs, where the partners have no
     appreciable sequence similarity, but one or both of them has
     appreciable sequence similarity with some other node in the other
     network. Formally, this is the number of aligned node pairs (ia,
     ib) with R[ia, ib] < epsilon but jb or ja exists, such that R[ia,
     jb] > epsilon or R[ja, ib] > epsilon.

_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)
       
       AnalyzeAlignment(A=ex$a, B=ex$b, R=ex$r, P=al, lookupNode,
         epsilon=.5)

