[BioC] GeneSetCollection using EntrezID

[Martin Morgan]

Hi Javier --

Javier Pérez Florido <jpflorido at gmail.com> writes:

> Dear list,
> I would like to carry out a Gene Set Analysis on the KEGG pathways on
> my Human Gene ST 1.0 array experiment using GSEABase. The annotation
> data included in this experiment is pd.hugene.1.0.st.v1, but it hasn't
> got functions like pd.hugene.1.0.st.v1PATH2PROBE. These functions are
> handled by hugene10sttranscriptcluster.db, so, my idea was to, first,
> using hugene10sttranscriptclusterENTREZID to get the entrezID for each
> gene in the experiment and then call GeneSetCollection using these
> entrezIDs, something like that:
>
> GeneSetCollection(entrezIDlist,
> idType="EntrezIdentifier",setType=KEGGCollection()), but it doesn't
> work
> Error en function (classes, fdef, mtable)  :
>   unable to find an inherited method for function "GeneSetCollection",
>   for signature "character", "character", "KEGGCollection"

Are you looking for something like the following from the help page
for GeneSetCollection?

  ## from KEGG identifiers, for example
  library(KEGG.db)
  lst <- head(as.list(KEGGEXTID2PATHID))
  gsc <- GeneSetCollection(mapply(function(geneIds, keggId) {
      GeneSet(geneIds, geneIdType=EntrezIdentifier(),
              collectionType=KEGGCollection(keggId),
              setName=keggId)
  }, lst, names(lst)))
          
but perhaps with

  lst <- head(as.list(KEGGEXTID2PATHID))

replaced by

  lst <- as.list(KEGGEXTID2PATHID[entrezIDlist])

Martin

>
> How can I build my Gene set object?
> Thanks,
> Javier
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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