[BioC] New Package: annaffy

[Colin A. Smith]

This summer I've written a new package that makes extensive use of 
the Bioconductor data packages to create annotated HTML and text 
files. It will take a vector or Affymetrix probe ids and generate a 
table with quite a bit of useful annotation data. It was mostly 
inspired by Robert Gentlemen's challenge found in the "ll.htmlpage" 
documentation:

"Details: A simple markup is used to provide clickable entries. 
Anyone that is energetic could greatly improve this."

The usefulness of the package essentially boils down to the function 
"aaf.summary". For an overview of what the package does, see the 
documentation for that function. For a quick example, run 
example(aaf.summary). There may be novel uses for the other functions 
in the package but they're mainly just slaves to the master function. 
In this version I haven't officially declared any of the functions 
private but I think I'll do that at some point soon.

annaffy depends on three Bioconductor packages: Biobase (only for the 
multiget function), GO, and KEGG (for second level annotation). Also, 
to really be useful for anything, it needs one of the other full 
annotation data packages available on the Bioconductor web site. I've 
tested it with the rgu34a package but I haven't gotten around to the 
other data packages yet.

To my knowledge, annaffy is Bioconductor compliant with the exception 
that I haven't written a vignette yet. It does pass R CMD check. 
There are most certainly still bugs, typos, and misspellings in the 
code/documentation. There is one big optimization I know of that 
still needs to be done. I would greatly appreciate any 
comments/suggestions/complaints. I haven't implemented functions that 
handle all the annotation data provided with the annotation packages. 
I am especially interested in finding out which of the other data 
sources would be useful and worth implementing.

-Colin

Source package:

http://homepages.nyu.edu/~cas277/annaffy_0.5.tar.gz

HTML page produced by example(aaf.summary):

http://homepages.nyu.edu/~cas277/affy.html
-- 

Colin Alexander Smith
cas277@nyu.edu

PGP Public Key:
  http://pgp.mit.edu:11371/pks/lookup?op=get&search=0x0B159DFF