ComputeM {GraphAlignment} | R Documentation |
Compute the score matrix M.
ComputeM(A, B, R, P, linkScore, selfLinkScore, nodeScore1, nodeScore0, lookupLink, lookupNode, clamp=TRUE)
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) |
clamp |
clamp values to range when performing bin lookups |
This function computes the score Matrix M from the network adjacency matrices A and B, the node similarity matrix R, an alignment P (given as a permutation vector) and the node and link scores with their associated binning information. The alignment P is either generated by the previous iterative step, or, initially, by using InitialAlignment. The matrix M is then given to the linear assignment solver to compute the new alignment.
The return value is the score matrix M.
Joern P. Meier, Michal Kolar, Ville Mustonen, Michael Laessig, and Johannes Berg
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) ComputeM(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)