Entering edit mode
4.6 years ago
Hi,
I have seen many posts about GO terms and GSEA but all are related to finding enriched GO terms from a DE gene list to the genome overall. I have a gene list that I can rank in hierarchical order or just list p-values as well if necessary that I wish to do GSEA but just on this DE gene list without using all genes that I pulled. I want to find the enriched GO terms just in this DE gene list. Is there a function that would let me do that in R?
All functions I have found so far like topGO and goseq for example requires the DE gene list as well as the full gene list as comparison to do GSEA.
Thank you in advance!
Can you clarify? Do you not want to use the entire transcriptome as the background? Pretty much any enrichment analysis requires some sort of background, whether it's a subset of genes (like only those expressed in your samples) or the entire transcriptome.