GO Enrichment Analysis in R – Count all the parents of each Term
I’m trying to implement a new GO tool in R.
After I have a list of genes, I’m using the following code to retrieve the relevant annotation for each gene:
AnnotationDbi::select(org.Hs.eg.db, keys = genes.list,
columns = c("ENTREZID", "GO"), keytype = id.type)
Once I compared the results to a published GO tool, it seems that the count for each gene is separate of its parents – meaning that each node in the org.Hs.eg.db database has a unique set of genes, which is not part of its parents genes.
If I understand correctly, a gene in one of the nodes should also appear in all of his ancestors.
The problem is when I’m trying to add all the ancestors of a term for each gene, in some cases where the same node has more than 1 parent (example below), I’m counting the ancestor more than once.
Is there any tool / database in r where each gene has it’s relevant GO terms all the way up in the tree, and the problem I mentioned above is fixed?
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