[BioC] GSEA GeneSetCollection

[Martin Morgan]

Hi Alice --

"Johnstone, Alice" <Alice.Johnstone at esr.cri.nz> writes:

> Hi
> I have been using the GSEA java version to look at my microarray
> results.  I ran into a problem as my samples are from rat.  I therefore
> want to create my own gene sets based on KEGG and GO information in the
> annotation packages.  I have used the command
> gsc<-GeneSetCollection(Data,setType=KEGGCollection())
> to create a collection, which is fine, but I want to be able to use this
> with the java version.. is it possible to create/export a gmx or gmt
> file from R from the GeneSetCollection object?

I don't think there's functionality available, but the following will
create a gmt file, I think (untested beyond file creation)

makeRow <- function(set)
    paste(setName(set), description(set),
          paste(geneIds(set), collapse="\t"),
          sep="\t")
writeLines(sapply(gsc, makeRow), "/tmp/rats.gmt")

Martin

> Thanks
>
> Alice Johnstone
>
> PhD Student
> Institute of Environmental Science and Research Ltd
> Kenepuru Science Centre
> 34 Kenepuru Drive
> PO Box 50-348
> Porirua
> New Zealand
>
> Tel:  + 64 4 914-0717
> Fax: + 64 4 914-0770
>
>
>
>> sessionInfo()
> R version 2.7.0 (2008-04-22) 
> i386-pc-mingw32 
>
> locale:
> LC_COLLATE=English_New Zealand.1252;LC_CTYPE=English_New
> Zealand.1252;LC_MONETARY=English_New
> Zealand.1252;LC_NUMERIC=C;LC_TIME=English_New Zealand.1252
>
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets
> methods   base     
>
> other attached packages:
>  [1] GSEABase_1.2.1        multtest_1.20.0       simpleaffy_2.16.0
> genefilter_1.20.0    
>  [5] survival_2.34-1       sma_0.5.15            rat2302probe_2.2.0
> rat2302cdf_2.2.0     
>  [9] MASS_7.2-41           gcrma_2.12.1          matchprobes_1.12.0
> illuminaRatBCv1_1.1.0
> [13] beadarray_1.8.0       affy_1.18.0           preprocessCore_1.2.0
> affyio_1.8.0         
> [17] geneplotter_1.18.0    annotate_1.18.0       xtable_1.5-2
> lattice_0.17-6       
> [21] limma_2.14.1          pcot2_1.8.0           amap_0.8-2
> rat2302.db_2.2.0     
> [25] AnnotationDbi_1.2.0   RSQLite_0.6-8         DBI_0.2-4
> Biobase_2.0.1        
> [29] rat2302_2.2.0        
>
> loaded via a namespace (and not attached):
> [1] cluster_1.11.10    graph_1.18.0       grid_2.7.0
> KernSmooth_2.22-22 RColorBrewer_1.0-2
> [6] XML_1.93-2.1
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793