def _get_pvals(pvalfnc_names, prt=sys.stdout):
fisher2pvals = {}
taxid = 10090 # Mouse study
file_obo = os.path.join(os.getcwd(), "go-basic.obo")
obo_dag = get_godag(file_obo, prt, loading_bar=None)
geneids_pop = GeneID2nt_mus.keys()
assoc_geneid2gos = get_assoc_ncbi_taxids([taxid], loading_bar=None)
geneids_study = get_geneid2symbol("nbt.3102-S4_GeneIDs.xlsx")
for fisher in pvalfnc_names:
goeaobj = GOEnrichmentStudy(geneids_pop,
assoc_geneid2gos,
obo_dag,
propagate_counts=False,
alpha=0.05,
methods=None,
pvalcalc=fisher)
fisher2pvals[fisher] = goeaobj.get_pval_uncorr(geneids_study, prt)
return fisher2pvals
