def expansion_list(self):
self.create_list_intra_extra()
self.__calculate_the_frequency()
self.calculate_TPFNFP()
self.statistical_result()
self.calculate_cutoff_frequency()
expansion_list = []
for key in self.list_extra:
freq = self.list_extra[key][0]
if freq >= self.cutoff_frequency:
gene_1, gene_2 = helper.decode_edge_key(key)
expansion_list.append([gene_1, gene_2, freq])
return expansion_list
def calculate_TPFNFP(self):
ncols = 100
# TP & FN
for key in self.list_intra:
gene_1, gene_2 = helper.decode_edge_key(key)
if self.__connection_is_in_lgn(gene_1, gene_2):
equal_point = int(math.floor(self.list_intra[key] * 100))
print equal_point
for i in range(equal_point, ncols):
self.TP[i] += 1
for i in range(0, equal_point):
self.FN[i] += 1
else:
for i in range(0, ncols):
self.FP[i] += 1
for key in self.list_extra:
equal_point = int(math.floor(self.list_extra[key][0] * 100))
for i in range(equal_point, ncols):
self.FP[i] += 1
def __refine_list_extra(self):
extra_genes = list(self.list_extra.keys())
for key in self.list_extra:
[_, extra_gene] = helper.decode_edge_key(key)
count = self.__count_appearance_of_extra_genes(extra_gene)
self.list_extra[key][1] = count
