[BioC] Go annotations

[Marc Carlson]

Hi Assa,

Did you try to use the Ontology() helper function?

Something like this:
library(GO.db)
Ontology(c("GO:0000003","GO:0000007"))

There are a series of helper functions like this for GO terms (Term, 
Ontology, Definition etc.)  You can read more about them in the man 
pages if you are interested.

I really hope this helps.  But I am having a little trouble 
understanding your email.  So if I have missed the mark then please give 
me a few more details about what you have and what you want to do.


   Marc



On 03/17/2011 08:07 AM, Assa Yeroslaviz wrote:
> Hi everybody,
>
> I have a problem working with GO annotations.
> I would like to group my data according to their GO categories, but only of
> one level.
> I have a data.frame (three columns: WT, mutation, mean(WT/mutation) and ca.
> 3150 rows)
> row.names    mut    WT    WT_mut
> 1737_Sepsecs    0.6924728    0.00728067    95.111137
> 1478_Ube2m    4.6102070    0.11428570    40.339316
> 2807_Pla2g4c    1.7234250    0.04276977    40.295400
> 2361_Trmt5    1.0203870    0.03652034    27.940238
>
> I also have the GO categories for each of this rows( the names are MGI
> symbols from the mouse genome).
>
> Unfortunately I have ALL the GO annotations. I would like to filter them
> according to the GO categories of a specific level(!). It doesn't matter
> whether 'MF', 'BP' or 'CC' yet.
> But I couldn't find anywhere a way of extracting just that.
>
> I would like to know whether there is a way of extracting GO annotations of
> a specific level from the GO annotation package.
>
> Thanks in advance
>
> Assa Yeroslaviz
>
> 	[[alternative HTML version deleted]]
>
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