tanghaibao/goatools

Idea: Flag to compute enrichment for user-specified GO terms

DylanSteinecke opened this issue · 0 comments

I want to compute the enrichment of a particular term without having to compute all other terms. This would save computational time, particularly because I want to run the enrichment analysis of a particular GO term multiple times in different sets of proteins. Currently, I do this by restricting it to the ontology of interest (BP, MF, CC) to save 2/3 of the time. After, I select the relevant GO term from the output file, but this is only after computing all the other terms' enrichment.

It would be convenient to have a flag for running the find_enrichment.py script (GoeaCliArgs args) such as "--term GO:0000001" or "-terms my_go_terms.txt" which would only compute the enrichment results for the GO term(s) of interest.

Thank you!