I have been asked to use python code to do the enrichment analysis using the hypergeomteric function below for a set of proteins:
getHypergeomPvalue(success_in_sample, sample_number, success_in_pop, pop_number):
if success_in_sample == 0: print '!!! Success in sample = 0, returning -1' return -1 p = hypergeom.pmf( numpy.arange(success_in_sample, sample_number+1), pop_number, success_in_pop , sample_number).sum() return p
I am a newbie to bioinformatics and this whole concept is like really new to me please if someone can help: 1: How do I construct a code using my protein data-set file and the KEGG pathways file and do the enrichment analaysis?
Thank you so much, need help desperately!!