[BioC] goTools: ontoCompare - GO list
Paquet, Agnes
apaquet at medsfgh.ucsf.edu
Thu Aug 23 21:27:47 CEST 2007
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
--
Passerelle antivirus IGF
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