[R] Help on comparing two matrices

Steve Lianoglou mailinglist.honeypot at gmail.com
Tue Aug 25 15:40:34 CEST 2009


It looks like you're getting more good stuff, but just to follow up:

On Aug 24, 2009, at 4:01 PM, Michael Kogan wrote:
> Steve: The two matrices I want to compare really are graph matrices,  
> just not adjacency but incidence matrices. There should be a way to  
> get an adjacency matrix of a graph out of its incidence matrix but I  
> don't know it...

If you're working with graph data, do yourself a favor and install  
igraph (no matter what solution you end up using for this particular  


In there, you'll find the `graph.incidence` function which creates a  
graph from its incidence matrix. You can then test if the two graphs  
are isomorphic.

That would look like so:

g1 <- graph.incidence(matrix.1)
g2 <- graph.incidence(matrix.2)
is.iso <- graph.isomorphic(g1, g2)
# Or, using the (somehow fast) vf2 algorithm
is.iso <- graph.isomorphic.vf2(g1, g2)


Steve Lianoglou
Graduate Student: Computational Systems Biology
   |  Memorial Sloan-Kettering Cancer Center
   |  Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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