ComputeM {GraphAlignment}R Documentation

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
linkScore link score matrix
selfLinkScore self link score matrix
nodeScore1 node score vector (s1)
nodeScore0 node score vector for unaligned nodes (s0)
lookupLink link bin lookup table
lookupNode node bin lookup table
clamp clamp values to range when performing bin lookups

Value

The return value is the score matrix M.

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)
[Package GraphAlignment version 1.0-0 Index]