[BioC] major alterations to GGdata/GGtools planned

Vincent Carey 525-2265 stvjc at channing.harvard.edu
Sat Mar 29 03:20:53 CET 2008

Now that David Clayton's snpMatrix package has entered Bioc
there are opportunities for substantial streamlining of
GGtools/GGdata.  The racExSet representation in use will not
be deleted, but the class for the main exemplars will involve
a more efficient representation using
snp.matrix objects.  This would lead to dramatic changes in
the GGdata package, which will use a whole-genome as
opposed to chromosome-specific representation.

Additionally, new independent resources for gene and snp locations
will allow removal of various metadata elements from the GGtools/
GGdata data stores.

Our standard approach is to deprecate for a cycle and then
remove, but I would like to remove the GGdata chr* objects
in one fell swoop.  Any GGdata/GGtools users who have objections to such a
change are invited to contact me off list for further discussions.
I will summarize back when discussions conclude.

Vince Carey, PhD
Assoc. Prof Med (Biostatistics)
Harvard Medical School
Channing Laboratory - ph 6175252265 fa 6177311541
181 Longwood Ave Boston MA 02115 USA
stvjc at channing.harvard.edu

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