Question: How to Perform Enrichment analysis on a protein list using KEGG pathways?
gravatar for KAZMI
2.4 years ago by
KAZMI0 wrote:

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!!

gsea python kegg pathways • 988 views
ADD COMMENTlink written 2.4 years ago by KAZMI0
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