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

[Robert Gentleman]

Zembower, Kevin wrote:
> 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.

   Very good point, I had not noticed that the DESCRIPTION file had not 
changed since we began - hopefully it is now somewhat more descriptive.

   You should be able to virtually everything in Wasserman and Faust 
from RBGL - I would be happy to hear about things that do not work, or 
where the implementation is not obvious.

   best wishes
     Robert

> 
> 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
> helpful.
> 
> -Kevin
> 
> -----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
> matrix?
> 
> Hi,
> 
> Zembower, Kevin wrote:
>> I'm interested in converting the graphNEL objects in the package
> SNAData
>> into adjacency matrices, so that I can convert them into 'network'
>> objects and use the R package 'sna' to analyze them. I'm working
> through
>> the examples in Wasserman and Faust, Social Network Analysis, and
> these
>> 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
> haven't
>> 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.
> 
>   Robert
> 
>> 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
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206-667-7700
rgentlem at fhcrc.org