ComputeScores: Compute scores
In GraphAlignment: GraphAlignment

Description Usage Arguments Details Value Author(s) Examples

Compute scores.

1 2	ComputeScores(A, B, R, P, linkScore, selfLinkScore, nodeScore1, nodeScore0, lookupLink, lookupNode, symmetric=TRUE, 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)
`symmetric`	network symmetry flag
`clamp`	clamp values to range when performing bin lookups

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).

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

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)
  
  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)