[BioC] Decomposing and recomposing BioConductor data sets

[Robert Gentleman]

On Fri, Jan 09, 2004 at 05:00:36PM +0100, Jarle Snertingdalen wrote:
> Hi
> 
> We're working on a project which uses R and other similar
> programs/languages to all sorts of computing. The project is written in
> Python, and we use RPy to communicate with R. However, data sets (like
> swirl) from BioConductor are not compatible with RPy. Through some
> research we found that they are made up of empty lists with a range of
> attributes attached to them.
> 
> I have to take apart the datasets, create 'clones' in python and then
> reconstruct them in R. The solution I have come up with so far is to
> recursively retrieve the attributes using 'attributes(foo)' and the
> 'foo$bar' syntax, place the retrieved attributes in a nested list, and
> convert the list to Python with RPy.

 They are S4 objects and you are not using the class and method
 definitions. You might want to look into the methods package a bit
 more, there is also John Chambers book, Programming with Data, and
 some notes on the developer page for the Bioconductor project. 

 Robert

> 
> My questions are: Why isn't the information put in nested lists in the
> first place, is my suggested approach valid for all BioConductor data
> sets, and is it the easiest way for generic decomposition of the data
> sets?
> 
> 
> regards,
> 
> Jarle Snertingdalen
> Software Developer http://www.zherlock.org
> NTNU Norway (Norwegian University of Science and Technology)
> 
> 
> PS: Some background information about the project; It is called SciCraft
> (formerly known as Zherlock), and is a graphical data analasys tool using
> third party software (like R and Octave) for computation. A typical use of
> the program could be to read data in R-format, use some Octave-function on
> the data read, then sending the data back into R for further work, and
> finally plot the results with some plot-tool and perhaps exporting it to
> some format. Whether a function is ran in R og Octave is invisible to the
> user.
> 
> _______________________________________________
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> Bioconductor at stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

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| Robert Gentleman                 phone : (617) 632-5250                   |
| Associate Professor              fax:   (617)  632-2444                   |
| Department of Biostatistics      office: M1B20                            |
| Harvard School of Public Health  email: rgentlem at jimmy.harvard.edu        |
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