def complete_mutexpairs(self, genepairs, p=0.05, maxOverlap=200, parallel_compute_number=0):
print "Generating list of", len(genepairs), " mutually exclusive hypotheses to test on permutation matrices..."
# Generate condition functions after analyzing each gene pair for Co-occurrence/min
mutex_set_condition_function_list = []
# Generate list of condition functions to test the permutation matrix for
for genepair in genepairs:
ConditionFunction = Condition(None)
condition_dict = {}
condition_dict['Genes'] = tuple(genepair)
condition_dict['Overlap'] = len(set.intersection(*[self.geneToCases_orig[gene] for gene in condition_dict['Genes']]))
condition_dict['Mutex'] = True
ConditionFunction.set_params([condition_dict])
mutex_set_condition_function_list.append((genepair, ConditionFunction))
print "Done. Now, calulating p-values of hypotheses..."
# Generate co-occurring pairs
if parallel_compute_number:
mutex_pair_to_pvalue = pac.parallel_compute_new(self.set_to_pvalue, [mutex_set_condition_function_list],
mutex_set_condition_function_list, 0, pac.partition_inputs, {0: pac.combine_dictionaries},
number=parallel_compute_number,
procnumber=parallel_compute_number)
else:
mutex_pair_to_pvalue = self.set_to_pvalue(mutex_set_condition_function_list)
print "Done. Now, finding mutually exclusive pairs"
# Generate dictionary for each pair. Optionally analyze each mutex set as well.
mpairsdict = {}
mgenedict = {}
for genepair in mutex_pair_to_pvalue:
if mutex_pair_to_pvalue[genepair] < p:
mstats = mex.analyze_mutex_set_new(self.numCases, self.geneToCases_orig, self.patientToGenes_orig,
geneset=tuple(genepair))
if mstats['Overlap'] <= maxOverlap:
mstats['PermutationProbability'] = mutex_pair_to_pvalue[genepair]
mpairsdict[genepair] = mstats
gene1, gene2 = tuple(genepair)
if gene1 not in mgenedict:
mgenedict[gene1] = set()
mgenedict[gene1].add(gene2)
else:
mgenedict[gene1].add(gene2)
if gene2 not in mgenedict:
mgenedict[gene2] = set()
mgenedict[gene2].add(gene1)
else:
mgenedict[gene2].add(gene1)
return mpairsdict, mgenedict
def complete_cooccurpairs(self, genepairs, p=0.05, minCooccur=1, min_cooccurrence_ratio=0.0, parallel_compute_number=0,
compute_scores=True):
"""
:param genepairs:
:param cprob:
:param minCooccur:
:param min_cooccurrence_ratio:
:param parallel_compute_number:
:return: cpairsdict, cgenedict
"""
print "Generating list of", len(genepairs), " co-occurring hypotheses to test on permutation matrices..."
# Generate condition functions after analyzing each gene pair for Co-occurrence/min
cooccur_set_condition_function_list = []
# Generate list of condition functions to test the permutation matrix for
for genepair in genepairs:
ConditionFunction = Condition(None)
condition_dict = {}
condition_dict['Genes'] = tuple(genepair)
condition_dict['Overlap'] = len(set.intersection(*[self.geneToCases_orig[gene] for gene in condition_dict['Genes']]))
condition_dict['Mutex'] = False
ConditionFunction.set_params([condition_dict])
cooccur_set_condition_function_list.append((genepair, ConditionFunction))
print "Done. Now, calulating p-values of hypotheses..."
# Generate co-occurring pairs
if parallel_compute_number:
cooccur_pair_to_pvalue = pac.parallel_compute_new(self.set_to_pvalue, [cooccur_set_condition_function_list],
cooccur_set_condition_function_list, 0, pac.partition_inputs, {0: pac.combine_dictionaries},
number=parallel_compute_number,
procnumber=parallel_compute_number)
else:
cooccur_pair_to_pvalue = self.set_to_pvalue(cooccur_set_condition_function_list)
print "Done. Now, finding co-occurring pairs"
# Generate dictionary for each pair. Optionally analyze each cooccur set as well.
cpairsdict = {}
cgenedict = {}
for genepair in cooccur_pair_to_pvalue:
if cooccur_pair_to_pvalue[genepair] < p:
cstats = mex.analyze_cooccur_set_new(self.numCases, self.geneToCases_orig, self.patientToGenes_orig,
geneset=tuple(genepair), compute_scores=compute_scores)
if cstats['Overlap'] >= minCooccur and cstats['CooccurrenceRatio'] >= min_cooccurrence_ratio:
cstats['PermutationProbability'] = cooccur_pair_to_pvalue[genepair]
cpairsdict[genepair] = cstats
gene1, gene2 = tuple(genepair)
if gene1 not in cgenedict:
cgenedict[gene1] = set()
cgenedict[gene1].add(gene2)
else:
cgenedict[gene1].add(gene2)
if gene2 not in cgenedict:
cgenedict[gene2] = set()
cgenedict[gene2].add(gene1)
else:
cgenedict[gene2].add(gene1)
return cpairsdict, cgenedict
