We wish to perform some enrichment (over representation) analysis of GWAS/QTL data distributed over a genome, is it possible with goseq?  I could not find any useful tutorials/manual -- could someone kindly show (1) required inputs (format, etc.; e.g. we have "trait names", "counts of reported significant GWAS/QTL with their genome chromosome/coordinate locations", "a small segments of a genome region to test"), (2) command line to run R/goseq (so that we can build a pipeline to run as routine), and (3) expected output? (e.g. p-value).

Hope I am not too naive by asking so :)

Zhiliang