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

Seth Falcon sfalcon at fhcrc.org
Thu Mar 15 17:57:26 CET 2007

"Simon Lin" <simonlin at duke.edu> writes:

> As suggested by Kyle, a translator among the identifiers could be very 
> helpful! Idealy, on the fly, but no need to be perfect. Ok to have mapping 
> errors in this process.
> I like the name of geneSet or geneList for the class.
> Methods associated with this class could be
> 1) a constructor, as mentioned by Kyle.
> 2) a translator: obtain other types of identifiers. USE CASE: give a set of 
> symbol, find entrezID in the mouse or rat genome.

These are interesting use cases that will really help us flesh out a
more complete API to the annotation data :-)

> 3) a method to "flat" the nested structure associated with the
>    class.

Not sure I follow you on the nested structure.

> The wiki by Seth on this topic is at
>   http://wiki.fhcrc.org/bioc/GeneSet_Class_Discussion
> By the way, I think the set_id and collection_id linking method
> needs some improvement. It allows nested structure, but it is hard
> to construct collections this way -- adding any new collections has
> to change all the pointers in each geneSet.

See the comment by Sean on the wiki.  I think we want set_id and
collection_id for compatibility with the Broad's data, but I think we
will represent relations between the objects externally -- that is,
have a collection object of some kind that contains the set_id's.  I
think that solves the issue you are concerned with.

Anyhow, check in on the wiki (the recent changes tab is helpful).


+ seth

Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center

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