def process_permutation(self): """ calculate the negsumlog10 values from the raw_p_values and add to right cluster in permutated_scores remove raw_p_values """ for cluster in self.raw_p_value.iterkeys(): if not cluster in self.permutated_scores: self.permutated_scores[cluster] = [] nsumlog10 = common.negsumlog10(self.raw_p_value[cluster]) self.permutated_scores[cluster].append(nsumlog10) #clean the raw p values for next permutation self.raw_p_value = {} return self.permutated_scores
def createcleanresults(self): """ summarize cluster_results and save it in self.clean_results """ for cluster in self.cluster_results.iterkeys(): current_cluster = self.cluster_results[cluster] n_snps = len(set(current_cluster["snp"])) n_genes = len(set((current_cluster["genes"]))) nsumlog10 = common.negsumlog10(current_cluster["p-value"]) self.clean_results[cluster] = {"n_snps":n_snps, "n_genes":n_genes, "sumneglog10":nsumlog10} return(self.clean_results)