Thank you, Martin.

That's what I need. I have a follow-up basic question.
How can I transform "collectionType"  to  character, such as "C2", in case I
only want to play with the sets from C2.
Cheers,
Di

On Wed, Jul 16, 2008 at 12:49 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> Hi Di --
>
> "Di Wu" <di.wu@med.monash.edu.au> writes:
>
> > Dear list,
> >
> > I am trying to use MsigDB, the gene set database from GSEA. I am
> interested
> > to know whether the sets of genes are from human or mouse, particularly
> in
> > C2.
> > I know I can always click the web and go deep to see how a set was
> obtained.
> > But is there any coding way to get the species sources for all the gene
> sets
> > in C2 or MsigDB.
>
> If you're using the GSEABase package, then each gene set read by
> getBroadSets records the organism, so for example
>
> > fl <- "/path/to/msigdb_v2.1.xml"
> > gss <- getBroadSets(fl) # read entire msigdb
> > organism(gss[[1]])
> "Human"
> > table(sapply(gss, organism))
>
>         Chimpanzee             Generic               Human
>                  1                 456                1769
> Human,Mouse,Rat,Dog               Mouse                 Pig
>                837                 248                  11
>                Rat              Rhesus          Zebra Fish
>                  3                   4                   8
>
> > # retrieve a few sets from the web
> > gss <- getBroadSets(asBroadUri(c('chr16q', 'GNF2_ZAP70')))
> > organism(gss[[1]])
> "Human"
>
> As a 'closer to the metal' alternative, you could use the XML package
>
> > xml <- xmlTreeParse(fl, useInternal=TRUE)
> > query <- '//GENESET[@STANDARD_NAME="KENNY_WNT_UP"]/@ORGANISM'
> > xpathApply(xml, query, xmlValue)
> [[1]]
> [1] "Mouse"
> > table(unlist(xpathApply(xml, "//@ORGANISM", xmlValue)))
>
>         Chimpanzee             Generic               Human
>                  1                 456                1769
> Human,Mouse,Rat,Dog               Mouse                 Pig
>                837                 248                  11
>                Rat              Rhesus          Zebra Fish
>                  3                   4                   8
>
> Martin
>
> > Appreciate your suggestions.
> > Cheers,
> > Di
> >
> >       [[alternative HTML version deleted]]
> >
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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
>

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