How To Get Dag Level Of A Gene Ontology Term Using Bioconductor

Question

[antgomo]

How to get the DAG tree level of a gene ontology term using R and Bioconductor? I looked and I couldn't find nothing in GO.db or related packages

Any ideas?

Thanks

[Damian Kao]

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.

[antgomo]

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

Answer 1

[hfang.shanghai]

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