[BioC] GeneSetCollection from GSEA

Sean Davis sdavis2 at mail.nih.gov
Wed Feb 27 12:40:20 CET 2008

On Wed, Feb 27, 2008 at 3:21 AM, Paul Christoph Schröder
<pschrode at alumni.unav.es> wrote:
> Hello all,
>  I'm using the GSEABase package For gene set enrichment I used the java software provided by the Broad Institute, but now since I want to use R I'm trying to implement it to my workflow.
>  If I'm interested only in a gene set collection like 'c2' from MSIGDB, what would be the appropiate command for getting the gene set collection?
>  I tried:
>  getBroadSets('msigdb_v2.1.xml', base="http://www.broad.mit.edu/gsea/donwloads.jsp")

Hi, Paul.

You need to specify the actual uri of the file that you want to get:

broadsets <- getBroadSets('ftp://ftp.broad.mit.edu/pub/gsea/msigdb_v2.1.xml')

That should do it for you.


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