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

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

gene bioconductor ontology r
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updated by Ram Ram • written by antgomo • antgomo

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.

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written by Damian Kao Damian Kao

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

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written by antgomo • antgomo

1 answer

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

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updated by Ram Ram • written by hfang.shanghai hfang.shanghai

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