def test_snmnmf(self): #import scipy as sp #import numpy as np #from pandas import DataFrame, Series ### get testing data ### m_rna, mi_rna, m2g_intction, pp_intction, bpGO = snmnmf.loadData( full=False) ### factorization ### # initialize the factorization snm = ns.NIMFA_SNMNMF(mRNA = m_rna, miRNA = mi_rna, DNAmethyl = None, gene2gene = pp_intction\ , miRNA2gene = m2g_intction, gene2DNAmethylation = None, params={'l1':0.1,'l2':0.1,'g1':0.1,'g2':0.1}) # run factorization snm.run(seed="random_c", rank=50, max_iter=5) # get factorization performance evaluation snm.performance.getResults() ### Results evaluation ### e = EnrichmentInGeneSets(snm) # get co-modules i = e.getGeneSets(T=1) ## compute enrichment in GO terms () enrich_bpGO = e.getEnrichmentInGeneSets(bpGO, T=0.1) # sort resultst accodring p-values sorted_enrich_bpGO = sorted(enrich_bpGO.iteritems(), key=operator.itemgetter(1)) # print results for key in sorted_enrich_bpGO: print key[0] + "\t:\t" + str(key[1]) ## compute enrichment ratio for different er_ratio = [e.getEnrichmentRatioInGeneSets(bpGO, T = 0.1, enrichment_threshold = 0.05, N = 100) \ for T in [0.1, 0.2, 0.5, 0.8, 1, 2, 5]]
def test_snmnmf(self): # import scipy as sp # import numpy as np # from pandas import DataFrame, Series ### get testing data ### m_rna, mi_rna, m2g_intction, pp_intction, bpGO = snmnmf.loadData(full=False) ### factorization ### # initialize the factorization snm = ns.NIMFA_SNMNMF( mRNA=m_rna, miRNA=mi_rna, DNAmethyl=None, gene2gene=pp_intction, miRNA2gene=m2g_intction, gene2DNAmethylation=None, params={"l1": 0.1, "l2": 0.1, "g1": 0.1, "g2": 0.1}, ) # run factorization snm.run(seed="random_c", rank=50, max_iter=5) # get factorization performance evaluation snm.performance.getResults() ### Results evaluation ### e = EnrichmentInGeneSets(snm) # get co-modules i = e.getGeneSets(T=1) ## compute enrichment in GO terms () enrich_bpGO = e.getEnrichmentInGeneSets(bpGO, T=0.1) # sort resultst accodring p-values sorted_enrich_bpGO = sorted(enrich_bpGO.iteritems(), key=operator.itemgetter(1)) # print results for key in sorted_enrich_bpGO: print key[0] + "\t:\t" + str(key[1]) ## compute enrichment ratio for different er_ratio = [ e.getEnrichmentRatioInGeneSets(bpGO, T=0.1, enrichment_threshold=0.05, N=100) for T in [0.1, 0.2, 0.5, 0.8, 1, 2, 5] ]
Created on Thu Jul 10 10:59:34 2014 @author: holecm """ from mixgene_project.wrappers.snmnmf import nimfa_snmnmf as ns import mixgene_project.wrappers.snmnmf.snmnmf as snmnmf from mixgene_project.wrappers.snmnmf.evaluation import EnrichmentInGeneSets import operator if __name__ == "__main__": # import scipy as sp #import numpy as np #from pandas import DataFrame, Series ### get testing data ### m_rna, mi_rna, m2g_intction, pp_intction, bpGO = snmnmf.loadData(full=False) ### factorization ### # initialize the factorization snm = ns.NIMFA_SNMNMF(mRNA=m_rna, miRNA=mi_rna, DNAmethyl=None, gene2gene=pp_intction \ , miRNA2gene=m2g_intction, gene2DNAmethylation=None, params={'l1': 0.1, 'l2': 0.1, 'g1': 0.1, 'g2': 0.1}) # run factorization snm.run(seed="random_c", rank=50, max_iter=5) # get factorization performance evaluation snm.performance.getResults() ### Results evaluation ### e = EnrichmentInGeneSets(snm) # get co-modules i = e.getGeneSets(T=1)
Created on Thu Jul 10 10:59:34 2014 @author: holecm """ from mixgene_project.wrappers.snmnmf import nimfa_snmnmf as ns import mixgene_project.wrappers.snmnmf.snmnmf as snmnmf from mixgene_project.wrappers.snmnmf.evaluation import EnrichmentInGeneSets import operator if __name__ == "__main__": # import scipy as sp #import numpy as np #from pandas import DataFrame, Series ### get testing data ### m_rna, mi_rna, m2g_intction, pp_intction, bpGO = snmnmf.loadData( full=False) ### factorization ### # initialize the factorization snm = ns.NIMFA_SNMNMF(mRNA=m_rna, miRNA=mi_rna, DNAmethyl=None, gene2gene=pp_intction \ , miRNA2gene=m2g_intction, gene2DNAmethylation=None, params={'l1': 0.1, 'l2': 0.1, 'g1': 0.1, 'g2': 0.1}) # run factorization snm.run(seed="random_c", rank=50, max_iter=5) # get factorization performance evaluation snm.performance.getResults() ### Results evaluation ### e = EnrichmentInGeneSets(snm) # get co-modules i = e.getGeneSets(T=1)