GOseq enrichment test

Question

[mujupas]

Hi!

I have a list of bed intervals, some of which intersect with protein coding genes (Refseq).

I'd like to use this Refseq genes list to run an enrichment test in GOseq, but I can't figure out how to skip the first steps of the standard GOseq workflow (given that I am not dealing with RNA-seq and/or differentially expressed genes).

Can anybody provide some help/tips?

Thank you in advance!

[Benn]

You can import your gene list as a target list, and all the genes of the genome as a background list. You'll have to make a gene.vector of this, as described in the user's guide. From there on it should work.