[BioC] Using GOstats for a non-model organism

[James W. MacDonald]

Hi Maureen,

On 2/14/2011 3:27 PM, Maureen J. Donlin wrote:
> Hi all,
>
> I'm new to R and have some very basic questions about using GOstats with
> a non-model organism.
> I'm trying to use the tutorial by Marc Carlson "How to Use GOstats
> and...with unsupported model organisms."
>
> I've created a GO to gene mapping file with the following 3 columns of
> data:
> Goterm Evidence GeneID
> GO:0015893 IEA CNAG_00003
> GO:0043231 IEA CNAG_00003
> GO:0015203 IEA CNAG_00003
> GO:0044425 IEA CNAG_00003
> ...
>
> I can import it using read.table, but I don't seem to be able to invoke
> the data frame correctly.

When you read it in using read.table(), you automatically have a 
data.frame.

>
> The tutorial reads:
> library("org.Hs.eg.db")
> frame = toTable(org.Hs.egGO)
> goFrameData = data.frame(frame$go_id, frame$Evidence, frame$gene_id)

Yep, this is just some code that Marc uses to create a data.frame so he 
can give an example.

>
> I imported the data into an object using read.table
>  >CneoGOanno <- read.table("Cneo_GOannot.txt")
>
> I tried to create a frame using:
>  > frame = toTable(CneoGOannot)
> Error in function (classes, fdef, mtable) :
> unable to find an inherited method for function "toTable", for signature
> "data.frame"
>
> Do I have to create some sort of database for this organism first? If
> so, what is it's format?
>
> Any suggestions would be most appreciated.

Just go to the next step, which will be something like

goFrame <- GOFrame(CneoGOanno, organism = "Cryptococcus neoformans")
goAllFrame <- GOALLFrame(goFrame)


Best,

Jim



>
> Regards,
> Maureen Donlin
>
> At the risk of too long of an email, here's the session info:
>  > sessionInfo()
> R version 2.12.1 (2010-12-16)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] org.Hs.eg.db_2.4.6 GOstats_2.16.0 RSQLite_0.9-4 DBI_0.2-5
> graph_1.28.0 Category_2.16.0 AnnotationDbi_1.12.0
> [8] Biobase_2.10.0
>
> loaded via a namespace (and not attached):
> [1] annotate_1.28.0 genefilter_1.32.0 GO.db_2.4.5 GSEABase_1.12.2
> RBGL_1.26.0 splines_2.12.1 survival_2.36-2 tools_2.12.1
> [9] XML_3.2-0 xtable_1.5-6
>
>

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues