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Gene-set for Wikipathways for R-GSEA (GMT format)
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nahush bhat  
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 More options Jun 12 2012, 10:47 pm
From: nahush bhat <nahush42...@gmail.com>
Date: Tue, 12 Jun 2012 19:47:17 -0700 (PDT)
Local: Tues, Jun 12 2012 10:47 pm
Subject: Gene-set for Wikipathways for R-GSEA (GMT format)
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Hi Everyone,

I am currently working on a R pipeline regarding Gene Set Enrichment
Analysis, I am using the R-GSEA package from the Broad Institute. There are
some gene-sets that came with the package. I was wondering if there was a
gene-set for Wikipathways available as it was'nt included in the package or
even if there is a way of getting it. The format I want it is in GMT
format. Any kinds of suggestions would be welcome.

Thanks in advance.


 
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Thomas Kelder  
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 More options Jun 14 2012, 7:56 am
From: Thomas Kelder <thomaskel...@gmail.com>
Date: Thu, 14 Jun 2012 13:56:03 +0200
Local: Thurs, Jun 14 2012 7:56 am
Subject: Re: [wp-discuss] Gene-set for Wikipathways for R-GSEA (GMT format)
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Hi Nahush,

There is currently no download option for GMT on the WikiPathways
website, but with some extra R code you can query the information from
the WikiPathways web service, store it in GSEABase compatible classes.
The GSEABase package provides you with a "toGMT" function that should
help you to write everything to GMT format.

Please take a look at the first part of the following code example,
hopefully that will help you getting started:
http://www.wikipathways.org/index.php/Help:WikiPathways_Webservice/Ge...

Best wishes,
Thomas


 
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