[BioC] goTools: ontoCompare - GO list

[Paquet, Agnes]

Hi Christelle,
 
ontoCompare provides several methods for counting the number of GO ids children to a top node. In your case, you can use the TIDS method, which returns the number of children of each node / total number of GO ids describing the group of proteins you provide in input.

 

You can use this method by changing the method aregument to "TIDS" when calling the function: 

ontoCompare(yourListofGOids,probeType="GO",method="TIDS",goType="BP")
 
Best,
 
Agnes
 

________________________________

From: bioconductor-bounces at stat.math.ethz.ch on behalf of Christelle Dantec
Sent: Thu 8/23/2007 9:13 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] goTools: ontoCompare - GO list



Hi,

I would like use ontoCompare on my list of proteins.
Then I have retrieved the GO Id for this list. I would like the
proportion in my list for BP-rank=1 (proportion in biological adhesion,
cell killing ...)

To illustrate my problem I take an example:
for a protein I can have 2 GO annotations for the BP type. But they can
provide from the same parent GO:0008150: Biological process.
So there will be a redundance for just one protein.
How can I resolve my problem?

Thanks a lot

Christelle




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Passerelle antivirus IGF
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