ComputeScores {GraphAlignment}R Documentation

Compute scores

Description

Compute scores.

Usage

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

Details

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).

Value

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

Author(s)

Joern P. Meier, Michal Kolar, Ville Mustonen, Michael Laessig, and Johannes Berg

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)
  
  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)

[Package GraphAlignment version 1.4.0 Index]