Exemplos de GOEnrichmentStudy._get_pval_uncorr em Python

Exemplo n.º 1

Arquivo: test_pvalcalc.py Projeto: tanghaibao/goatools

def _get_pvals(pvalfnc_names, prt=sys.stdout):
    fisher2pvals = {}
    taxid = 10090  # Mouse study
    obo_dag = GODag(download_go_basic_obo(prt=prt))
    geneids_pop = GeneID2nt_mus.keys()
    assoc_geneid2gos = get_assoc_ncbi_taxids([taxid])
    geneids_study = _get_geneid2symbol("nbt.3102-S4_GeneIDs.xlsx", prt)
    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

Exemplo n.º 2

def _get_pvals(pvalfnc_names, prt=sys.stdout):
    fisher2pvals = {}
    taxid = 10090  # Mouse study
    obo_dag = GODag(download_go_basic_obo(prt=prt))
    geneids_pop = GeneID2nt_mus.keys()
    assoc_geneid2gos = get_assoc_ncbi_taxids([taxid])
    geneids_study = _get_geneid2symbol("nbt.3102-S4_GeneIDs.xlsx", prt)
    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