ComputeLinkParameters {GraphAlignment}R Documentation

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

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.

Value

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

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)

[Package GraphAlignment version 1.4.0 Index]