Question: How To Get Dag Level Of A Gene Ontology Term Using Bioconductor
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gravatar for antgomo
6.2 years ago by
antgomo30
Spain
antgomo30 wrote:

How to get the DAG tree level of a gene ontology term using R and Bioconductor? I looked and I could'nt find nothing in GO.db or related packages

Any ideas?

Thanks

gene R bioconductor ontology • 2.4k views
ADD COMMENTlink modified 4.7 years ago by hfang.shanghai140 • written 6.2 years ago by antgomo30

One potential problem you'll face is that there really is no "level" in the GO DAG as it is not a strictly hierarchical structure, ie. a child node can have multiple parent nodes, there are several paths to the same node. You can try to define the level by the number of nodes in the shortest path it takes to get to the node or longest path, or average number of nodes....etc. It might not be the best metric to use.

ADD REPLYlink modified 6.2 years ago • written 6.2 years ago by Damian Kao15k

OK; I see, thanks Damian, I'll try to face the problem converting the GO terms as a graph and getting the path

ADD REPLYlink written 6.2 years ago by antgomo30
0
gravatar for hfang.shanghai
4.7 years ago by
United Kingdom
hfang.shanghai140 wrote:

It has been supported in the 'dnet' package: http://supfam.org/dnet/visDAG.html

ADD COMMENTlink written 4.7 years ago by hfang.shanghai140
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