[Bioc-devel] GSEABase: classes for gene set manipulation

Martin Morgan mtmorgan at fhcrc.org
Wed May 30 22:52:01 CEST 2007

DevelopeRs -- 

GSEABase is a new package for representing gene set data. A
preliminary version is available in the Bioconductor devel branch

The main classes are GeneSet (for representing sets of genes) and
GeneColorSet (for genes 'colored' in relation to a phenotype, e.g.,
UP-regulated genes are associated with ELEVATED levels of a
phenotype). Main functionality includes construction (e.g., from
ExpressionSet or other gene lists, or from XML following the Broad
format), and logical (set) operations.

The best introduction is probably in

> class?GeneSet

Any feedback would be great; I expect the classes to change over the
next week or so as we figure out what is useful and what not, and for
additional functionality (e.g., sub setting!) to be implemented.

The package developed from great input generated on this mailing list
a couple of months ago, and from input and workshops at the
Bioconductor Developer meeting held in Lausanne, Switzerland on April
4 and 5. Notes from these conversations are at 


Martin Morgan
Bioconductor / Computational Biology

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