topGo analysis with PANTHER.db

Question

[chuliangcui]

Hi, I have a list of sig changed genes from staphylococcus aureus and want to do the go enrichment analysis with topGo in R. However there is no database for Staph on the website. Meanwhile I found Panther.db has species as staphylococcus aureus and can perform go analysis on line. (http://geneontology.org/) But i want to perform this in R. I can access the database in R: BiocManager::install("PANTHER.db"). But it is not accepted by topGo. Could anyone give me some suggestion how to do this in R instead of copying paste list of gens to the website? Thanks

Answer 1

[biofalconch]

Have a look at section 4.3 of the manual, it might help