def _run_multitest_local(self, ntmt): """Use multitest mthods that have been implemented locally.""" corrected_pvals = None method = ntmt.nt_method.method if method == "bonferroni": corrected_pvals = Bonferroni( ntmt.pvals, ntmt.alpha).corrected_pvals elif method == "sidak": corrected_pvals = Sidak(ntmt.pvals, ntmt.alpha).corrected_pvals elif method == "holm": corrected_pvals = HolmBonferroni( ntmt.pvals, ntmt.alpha).corrected_pvals elif method == "fdr": # get the empirical p-value distributions for FDR term_pop = getattr(self, 'term_pop', None) if term_pop is None: term_pop = count_terms(self.pop, self.assoc, self.obo_dag) p_val_distribution = calc_qval(len(ntmt.study), self.pop_n, self.pop, self.assoc, term_pop, self.obo_dag) corrected_pvals = FDR(p_val_distribution, ntmt.results, ntmt.alpha).corrected_pvals self._update_pvalcorr(ntmt, corrected_pvals)
def _run_multitest_local(self, ntmt): """Use multitest mthods that have been implemented locally.""" corrected_pvals = None method = ntmt.nt_method.method if method == "bonferroni": corrected_pvals = Bonferroni(ntmt.pvals, ntmt.alpha).corrected_pvals elif method == "sidak": corrected_pvals = Sidak(ntmt.pvals, ntmt.alpha).corrected_pvals elif method == "holm": corrected_pvals = HolmBonferroni(ntmt.pvals, ntmt.alpha).corrected_pvals elif method == "fdr": # get the empirical p-value distributions for FDR term_pop = getattr(self, 'term_pop', None) if term_pop is None: term_pop = count_terms(self.pop, self.assoc, self.obo_dag) p_val_distribution = calc_qval(len(ntmt.study), self.pop_n, self.pop, self.assoc, term_pop, self.obo_dag) corrected_pvals = FDR(p_val_distribution, ntmt.results, ntmt.alpha).corrected_pvals self._update_pvalcorr(ntmt, corrected_pvals)