[BioC] Find enriched GO terms, given a list of GO terms of interest and background GO terms

[JJ [guest]]

I have annotated some genomes with my own protein function annotation pipeline. Each genome will have a list of genes and their corresponding GO terms. In my annotation, the GO terms are on all kinds of different levels because of the hierarchical structure of GO itself. 

So my input will be all the GO terms for one (or a few) genome of interest, and a bigger set of background GO terms. I would like to figure out which GO terms are enriched in the interesting genomes and what they do.

It'll be great if I could also specify on what level the GO terms are summarized.

Can topGO handle this kind of problem? If not, any suggestions?

Thanks a lot!

-JJ





 -- output of sessionInfo(): 

R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] grid      parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] AnnotationForge_1.4.4 org.Hs.eg.db_2.10.1   GOFunction_1.10.0     Rgraphviz_2.6.0      
 [5] ALL_1.4.16            topGO_2.14.0          SparseM_1.03          GO.db_2.10.1         
 [9] RSQLite_0.11.4        DBI_0.2-7             AnnotationDbi_1.24.0  Biobase_2.22.0       
[13] BiocGenerics_0.8.0    graph_1.40.1          BiocInstaller_1.12.0 

loaded via a namespace (and not attached):
[1] IRanges_1.20.6  lattice_0.20-24 stats4_3.0.2    tools_3.0.2 

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