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)
