for total_sig in total_sig_hypotheses
]
def simultaneousPermutation(significance_level, n, categories, testset_size,
iterations):
result = simultaneousPermutationWithMultipleSignificanceLevels(
[significance_level], n, categories, testset_size, iterations)
return result[0]
if __name__ == "__main__":
n = 40
iterations = 1000
fisher.init(n)
testset = set([0, 1, 4, 7, 2, 10, 40, 32])
categories = [
set([0, 1]),
set([1, 4, 7, 0, 2, 10, 40]),
set([10, 2, 40]),
set([32])
]
cat_pvalues = [computeOverlapPval(s, testset, n) for s in categories]
levels = [0.1, 0.05, 0.01, 0.005]
perm_DR = simultaneousPermutationWithMultipleSignificanceLevels(
levels, n, categories, len(testset), iterations)
print "\nLoading drug bank database from XML..."
drugDB.loadXML(os.sep.join(["data","drugbank","drugbank.xml"]))
drugDB.mapTargetNames(os.sep.join(["data","drugbank","target_links.csv"]))
else:
import drugbankCatalog as drugDB
print "\nLoading DrugBank drug catalogue..."
drugDB.initDruglist(os.sep.join(["data","drugbank","drug_links.csv"]))
print "\nLoading DrugBank drug target catalogue..."
drugDB.initTargets(os.sep.join(["data","drugbank","target_links.csv"]), os.sep.join(["data","drugbank","all_target_protein.fasta"]),__ENABLE_GENE_VERIFICATION,__ENABLE_GENE_UPDATES)
commonGenes = studyGenes & gwasDB.__geneSet
cgWithoutGWAS = studyGenes - gwasDB.__geneSet
gwasWithoutCG = gwasDB.__geneSet - studyGenes
print "initializing fisher algorithm..."
fisher.init(len(geneDB.__approved_symbols))
# chi-square contingency table for gwas and RE
a1 = len(commonGenes)
b1 = len(gwasWithoutCG)
c1 = len(cgWithoutGWAS)
d1 = len( geneDB.__approved_symbols - (studyGenes | gwasDB.__geneSet) )
oddsratio1 = geneUtils.oddsRatio(a1,b1,c1,d1)
kappa1 = geneUtils.kappaStatistic(a1,b1,c1,d1)
fisher_exact1 = fisher.compute(a1,b1,c1,d1)
fisherp1 = fisher.significance(fisher_exact1, a1,b1,c1,d1)
commonDrugTargets = drugDB.__geneSet & studyGenes
