GraphAlignment (version 1.36.0)

ComputeM: Compute score matrix M

Description

Compute the score matrix M.

Usage

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

Arguments

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

Value

The return value is the score matrix M.

Details

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.

Examples

  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)