def do_bootstrap():
"""
Do a bootstrap analysis on GO p-values.
"""
logging.info(
'Running GO bootstrap analysis with %d samples: topGO method=%s',
options.num_bootstrap_samples, options.topgo_method)
transcriptional_programs, factor_universe, target_universe = tp_threshold.threshold_tps(
)
genes_2_GO, go_context = go.initialise_go_context(factor_universe,
target_universe,
options.go_ontologies)
tp_sizes = filter(
None, map(len, (tp.targets for tp in transcriptional_programs)))
p_values = list()
for sample in generate_bootstrap_samples(options.num_bootstrap_samples,
target_universe, tp_sizes):
go_analysis = dict(
(ontology,
go.try_go_analysis(go_data, sample, 1., options.topgo_method))
for ontology, go_data in go_context.targets_go_data.iteritems())
best_p_value = min(
map(topgo.p_value_from_r,
map(topgo.best_p_value, go_analysis.values())))
p_values.append(best_p_value)
logging.info('GO bootstrap analysis completed')
return p_values
def do_bootstrap():
"""
Do a bootstrap analysis on GO p-values.
"""
logging.info('Running GO bootstrap analysis with %d samples: topGO method=%s', options.num_bootstrap_samples, options.topgo_method)
transcriptional_programs, factor_universe, target_universe = tp_threshold.threshold_tps()
genes_2_GO, go_context = go.initialise_go_context(factor_universe, target_universe, options.go_ontologies)
tp_sizes = filter(None, map(len, (tp.targets for tp in transcriptional_programs)))
p_values = list()
for sample in generate_bootstrap_samples(options.num_bootstrap_samples, target_universe, tp_sizes):
go_analysis = dict(
(
ontology,
go.try_go_analysis(
go_data,
sample,
1.,
options.topgo_method
)
)
for ontology, go_data
in go_context.targets_go_data.iteritems()
)
best_p_value = min(map(topgo.p_value_from_r, map(topgo.best_p_value, go_analysis.values())))
p_values.append(best_p_value)
logging.info('GO bootstrap analysis completed')
return p_values
def go_analysis():
logging.info('Running GO analysis: p-value threshold=%e; topGO method=%s',
options.go_p_value_threshold, options.topgo_method)
transcriptional_programs, factor_universe, target_universe = tp_threshold.threshold_tps(
)
genes_2_GO, go_context = go.initialise_go_context(factor_universe,
target_universe,
options.go_ontologies)
go_analyses = list()
f = open(os.path.join(options.output_dir, 'go-analyses.txt'), 'w')
for tp in transcriptional_programs:
go_analysis = go.TPGoAnalysis(tp, go_context,
options.go_p_value_threshold,
options.topgo_method)
go_analysis.print_go_analyses(f,
options.go_p_value_threshold,
log=True)
go_analysis.print_go_analyses(sys.stdout, options.go_p_value_threshold)
go_analyses.append(go_analysis)
f.close()
write_latex(go_analyses)