ComputeLinkParameters: Compute link parameters
In GraphAlignment: GraphAlignment

Description Usage Arguments Details Value Author(s) Examples

Compute the optimal scoring parameters (link score) for a given alignment.

1	ComputeLinkParameters(A, B, P, lookupLink, clamp=TRUE)

`A`	adjacency matrix for network A
`B`	adjacency matrix for network B
`P`	permutation vector (see InitialAlignment, AlignNetworks)
`lookupLink`	link bin lookup table (see GetBinNumber)
`clamp`	clamp values to range when performing bin lookups

This function computes optimal link score parameters for use with ComputeM and AlignNetworks. It takes two matrices as well as an initial alignment P and the lookup table for link binning, lookupLink, as parameters.

The return value is a list containing the self link score matrix (lsSelf) and the link score matrix (ls).

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)