tl;dr: Is there an accessor function for getting GO to gene mapping from a topGOdata object? The printGenes function doesn't work with my case.
Full explanation
I'm doing gene set enrichment analysis in topGO for a bacterial strain that does not have an annotation package. I can provide my own annotation, and use the gene2GO functionality of topGO. I am able to run enrichment tests using runTest and get an output table with GenTable.
I would like to access the genes associated with some of the enriched GO terms. These data are contained in the topGOdata object. Are there simple accessor functions for getting these data? I know that the function printGenes can return the list of genes along with other info, but printGenes requires a chip, which this custom annotation doesn't have.
I have no experience with this myself, but this (old) thread may be of relevance? How to retreive topGO significant IDs of genes after enrichment test ?
That's it! I had missed the
genesInTerm()function mentioned in that post- it returns exactly what I was looking for.Thanks!