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