--- a
+++ b/matlab_source/netics_fun_all.m
@@ -0,0 +1,28 @@
+%script that prioritize genes by taking the mean ranked position across several values of the restart probability
+%store final ranked list of genes in ranked_list_genes
+
+fidnet = fopen('network_genes.txt','r');
+g = textscan(fidnet, '%s', 'delimiter', '\n');
+network_genes = g{1};
+fclose(fidnet);
+
+load('adj_lar_com');
+betas = .2:.1:.8;
+
+ranked_list_genes_breast = cell(length(betas),1);
+for i = 1:length(betas),
+    disp(strcat('Restart Probability = ',num2str(betas(i))));
+    ranked_list_genes_breast{i} = netics_fun( 'mutation_data_breast.txt', adj_lar_com, betas(i), 'RANK_AGGREG=SUM', 'network_genes.txt', 'RNA_diff_expr_breast.txt', 'protein_diff_expr_breast.txt');
+end
+
+ranks = zeros(1,length(network_genes));
+for i = 1:length(network_genes),
+    pos = zeros(1,length(betas));
+    for j = 1:length(betas),
+        pos(j) = find(ismember(ranked_list_genes_breast{j},network_genes{i}));
+    end
+    ranks(i) = mean(pos);
+end
+
+sorted = sortrows([ranks; 1:length(ranks)]');
+ranked_list_genes = network_genes(sorted(:,2));