GO Enrichment Analysis in R - Count all the parents of each Term

Question

[rrapopor]

Hi,

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:

library(AnnotationDbi)

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?

Thank you!