[BioC] Romer and symbols2indices query

[Loren Engrav]

Am back

So I have romer and GSEABase running via previous help thank you, but while
running I explore GSEABase

And I have a lesser question for interest

In GSEABase I do
 gmtObject <- getGMT("c2all.v2.5.symbols.gmt",
collectionType=BroadCollection(category="c2"), geneType=SymbolIdentifier())
 which finishes without error
Then
 class(gmtObject) is GeneSetCollection

How do I convert gmtObject to a list of gene sets as required in romer when
using
X <- symbols2indices (ListOfGeneSets, MYsymbols)



From: Vincent Carey <stvjc at channing.harvard.edu>
Date: Tue, 4 May 2010 11:40:39 -0400
To: Loren Engrav <engrav at u.washington.edu>
Cc: rbioc <bioconductor at stat.math.ethz.ch>
Subject: Re: [BioC] Romer and symbols2indices query

Very briefly, the GSEABase package has relevant utilities for gmt file
import/export and may be worth considering for these tasks.

On Tue, May 4, 2010 at 10:43 AM, Loren Engrav <engrav at u.washington.edu>
wrote:
> Thank you, got it
> 
> Downloading rdata objects saves reading them into an rdata object, cool
> 
> But for interest, in R/GSA there is
> GSA.read.gmt(filename.gmt) to read in a .gmt file
> 
> Does limma or romer have an equivalent function?
> 
> 
>> From: Matthew Ritchie <mritchie at wehi.EDU.AU>
>> Date: Tue, 4 May 2010 14:44:23 +1000 (EST)
>> To: Loren Engrav <engrav at u.washington.edu>
>> Cc: rbioc <bioconductor at stat.math.ethz.ch>
>> Subject: Re: [BioC] Romer and symbols2indices query
>> 
>> Dear Loren,
>> 
>> You can find rdata objects of the Broad's MSigDB gene sets at
>> 
>> http://bioinf.wehi.edu.au/software/MSigDB/index.html
>> 
>> You are right, the 'symbols' argument in the function symbols2indicies()
>> are the gene symbols corresponding to the probes from your microarray
>> data.
>> 
>> For example, to use the human C2 collection, download the rdata file, then
>> run the following.
>> 
>> load("human_c2.rdata")
>> c2 = symbols2indices(Hs.gmtl.c2, symbols)
>> 
>> (this assumes 'symbols' is a vector containing the gene symbols from your
>> array data)
>> 
>> Best wishes,
>> 
>> Matt
>> 
>>> Have done GSEA and GSA for set enrichment and am setting out to try romer
>>> and have probably "simple" question
>>> 
>>> To get the Broad set into a list of indices there is
>>> symbols2indices(gmtl.official, symbols) but
>>> 
>>> 1)how do I get the Broad set into gmtl.official? And
>>> 2)is symbols a vector of MY probe sets of interest?
>>> 
>>> I checked gmane and found only one comment about romer
>>> Also checked limma reference pdf
>>> 
>>> Thank you
>> 
>> 
>> ______________________________________________________________________
>> The information in this email is confidential and inte...{{dropped:7}}
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor