[BioC] GeneSetCollection with GOCollection and ontology argument

[Martin Morgan]

On 11/16/2012 01:45 AM, Michael Love wrote:
> hi,
>
> I am trying to use the GeneSetCollection function to retrieve the BP GO
> gene sets over some Entrez genes.  But it seems like the ontology
> argument of GOCollection is not making a difference to which terms are
> in the resulting GeneSetCollection.  In the help for GOCollection it
> says " Unlike evidence code, ontology membership is enforced when
> GOCollection gene sets are constructed."  so I expected that the
> resulting object would only have BP GO terms.

Hi Michael -- sorry for the delayed response. This has been addressed in release 
v. 1.20.1 and devel version v. 1.21.1; devel requires graph >= 1.37.2) and 
R-devel. These are available from svn now, via biocLite all being well Sunday 
after 10am Seattle time.

I'm interested in updating GSEABase so bug reports and feedback (especially on 
the devel version) welcome; there are some serious performance issues that 
unfortunately require a substantial revision.

Martin

>
> thanks for any guidance,
>
> a small example for the Entrez genes 1-20:
>
> library(org.Hs.eg.db)
> library(GSEABase)
> gsc <- GeneSetCollection(as.character(1:20),
> idType=AnnotationIdentifier("org.Hs.eg.db"),
> setType=GOCollection(ontology="BP"))
> table(unlist(eapply(GOTERM[names(gsc)],slot,"Ontology")))
>
>    BP  CC  MF
> 101  26  44
>
>   > sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>    [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>    [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>    [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>    [7] LC_PAPER=C                 LC_NAME=C
>    [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods base
>
> other attached packages:
>    [1] GO.db_2.7.1          GSEABase_1.20.0      graph_1.36.1
>    [4] annotate_1.34.0      org.Hs.eg.db_2.8.0   RSQLite_0.11.1
>    [7] DBI_0.2-5            AnnotationDbi_1.20.2 Biobase_2.18.0
> [10] BiocGenerics_0.4.0   BiocInstaller_1.8.3
>
> loaded via a namespace (and not attached):
> [1] IRanges_1.16.4  parallel_2.15.0 stats4_2.15.0   tools_2.15.0
> [5] XML_3.9-4       xtable_1.7-0
>
> ...also I tried for:
>
>   > sessionInfo()
> R Under development (unstable) (2012-11-01 r61067)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>    [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>    [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>    [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>    [7] LC_PAPER=C                 LC_NAME=C
>    [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets methods
> [8] base
>
> other attached packages:
>    [1] GO.db_2.8.0          org.Hs.eg.db_2.8.0   RSQLite_0.11.2
>    [4] DBI_0.2-5            GSEABase_1.21.0      graph_1.37.1
>    [7] annotate_1.37.1      AnnotationDbi_1.21.5 Biobase_2.19.0
> [10] BiocGenerics_0.5.1   Defaults_1.1-1       BiocInstaller_1.9.4
>
> loaded via a namespace (and not attached):
> [1] IRanges_1.17.13 stats4_2.16.0   tools_2.16.0    XML_3.95-0.1
> [5] xtable_1.7-0
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>


-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793