[Bioc-devel] A geneSet data class for facilitating GSEA

Vincent Carey 525-2265 stvjc at channing.harvard.edu
Wed Mar 14 15:19:36 CET 2007

i like this idea in principle.  the RGenetics folks may have done
something in this direction.

you might want to have geneList as an abstract class, and then
extend to EntrezGeneList, RefseqGeneList and so forth so that
dispatch could work without looking into the idType ...

a version or date field might also be important

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

On Wed, 14 Mar 2007, Sean Davis wrote:

> GSEA, both the specific method and the general concept, is becoming more
> prevalent and important in data analysis.  There have been several mentions
> of including various "gene lists" for use with Category or other methods.  Is
> there interest in making a generic geneSet class for storing such
> information?  (Or does it already exist and I just haven't seen it?)  I bring
> this up because I think it could be quite useful to have a general solution
> for the community (like the eSet class has become).  A class could be as
> simple as a vector of Entrez Gene IDs to something more complicated (but
> perhaps a bit more useful for general consumption) like:
> identifier: an identifier for the set (perhaps from a public database like
> MSigDB)
> title:  One line title
> description: free text description
> species: The species to which the dataset applies
> URL: from where the data were derived
> MIAME: class "MIAME" object
> protocol: (could be in MIAME, also) description of methods to produce genelist
> from raw data source
> idType:  What type of ID is stored (Entrez, Refseq, Ensembl, etc)?
> geneList: vector of IDs
> A simple wrapper data structure (even just a list) could then be used to
> distribute the geneSets.  Some methods could then be defined for converting
> to an incidence matrix for use by Category, etc.  But I think the most
> important points from above are 1) maintaining some metadata about the
> genelists and 2) standardization to reduce duplicated work.  Individual
> groups would then instantiate the geneSets using whatever means they see fit
> (parsing MSigDB, IPI files, etc.).
> Any thoughts?
> Sean
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