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)
