GraphAlignment (version 1.36.0)

ComputeLinkParameters: Compute link parameters

Description

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

Usage

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

Arguments

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

Value

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

Details

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.

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)