[BioC] Example of converting graphNEL object to ajacency matrix?

Zembower, Kevin kzembowe at jhuccp.org
Thu Apr 24 16:07:42 CEST 2008

Robert and Gabor, thanks so much for writing and helping me. Both
suggestions will be very helpful.

Robert, with regard to RBGL, I didn't consider this because I'm not very
knowledgeable about projects in the Bioconductor system. In fact, my
only interest was caused by Googling 'krackhardt' and discovering his
data in the SNAData package. I've never heard of RBGL, but Googling it
just now returns a page with "Description: demo of interface with full
copy of all hpp defining boost." From this description, I don't think
that I would have known that this has anything to do with Social Network
Analysis. I've printed the manual for RBGL and will investigate it for
my use. Thanks for suggesting this.

I also didn't know that 'as' was an alias for 'coerce.' Thank you so
much for pointing this out, and for your example. All of this is really


-----Original Message-----
From: Robert Gentleman [mailto:rgentlem at fhcrc.org] 
Sent: Thursday, April 24, 2008 9:29 AM
To: Zembower, Kevin
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Example of converting graphNEL object to ajacency


Zembower, Kevin wrote:
> I'm interested in converting the graphNEL objects in the package
> into adjacency matrices, so that I can convert them into 'network'
> objects and use the R package 'sna' to analyze them. I'm working
> the examples in Wasserman and Faust, Social Network Analysis, and
> datasets will save me considerable typing.

   Why not just analyze them with the tools in RBGL (which are a bit 
more extensive than those in sna)?

> I think that this is possible because of references to the 'coerce'
> method on the graphNEL-class and graphAM-class help pages, but I
> been successful. I've tried commands like:
> coerce(friendship, fs-mat)
> coerce(friendship, fsmat)
> as.matrix(friendship)
> as.graphAM(friendship)
> coerce(from="friendship", to="fsmat")

   I am a bit confused about how you got to any of these incantations. 
The man page for coerce (as) is pretty explicit about needing to specify

the input, and the name of the desired class, so my first guess would 
have been:

   as(friendship, "matrix")

  which does indeed seem to work.


> Can anyone give me an example of converting a graphNEL object to a
> regular matrix, such as an adjacency matrix? I think with just one
> example, I could work things out.
> Thanks for your advice and suggestions.
> -Kevin
> Kevin Zembower
> Internet Services Group manager
> Center for Communication Programs
> Bloomberg School of Public Health
> Johns Hopkins University
> 111 Market Place, Suite 310
> Baltimore, Maryland  21202
> 410-659-6139 
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Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
rgentlem at fhcrc.org

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