geneCorr_NEW.m

%%%--Correlation between the expression pattern of all pairs of Genes at
%%% different on spatial expression at different age groups

clear all;

%%% Calculate the gene correlation networks for each donor separately
% load('files\donorsExpMat_5RPKM.mat');
% 
% donorsExpMat_5RPKM = normalizeExpMat(donorsExpMat_5RPKM);
% donorsExpMat_5RPKM = donorsExpMat_5RPKM + rand(size(donorsExpMat_5RPKM))*(10^-5);
% 
% for i = 1 : size(donorsExpMat_5RPKM, 3)
% 
%     clear geneMat;
%     
%     geneMat = donorsExpMat_5RPKM(:,:,i); 
%     geneMat = geneMat';
%         
%     RHO= corr(geneMat, 'Type', 'Spearman');
% 
%     outFile = ['results\geneCorr\Avg(log2+epsilon)\donor' num2str(i)];
%     save(outFile, 'RHO');
% 
%     clear RHO;
%     
% end

%%% Calculate the average gene correlation per age Group
group{1} = [1, 2, 3 ,4];
group{2} = [5, 6, 7, 8];
group{3} = [9, 10, 11, 12];
group{4} = [13, 14, 15, 16];
group{5} = [17, 18, 19, 20];
group{6} = [21, 22, 23, 24];
group{7} = [25, 26, 27, 28, 29, 30];

folder = ['results\geneCorr\Avg(log2+epsilon)\'];

for i = 1 : length(group)
    
    clear tg;
    tg = group{i}; 
    
    for j = 1 : length(tg)
        
        load([folder 'donor' num2str(tg(j))]);
        corrVol(:,:,j) = RHO;
        clear RHO;
        
    end
    
    corrMat = mean(corrVol, 3);
    clear corrVol;
    
    save(['results\geneCorr\Avg(log2+epsilon)\ageGroup' num2str(i) '_corrMat.mat'], 'corrMat');
%     csvwrite(['results\geneCorr\Avg(log2+epsilon)\ageGroup' num2str(i) '_corrMat.csv'], corrMat);
    clear corrMat;

end
%%%------------------------------------------------------------------------

%%% Calculate the gene correlation networks for concatenated samples
% load('files\newGeneMat_refined.mat');
% 
% for i = 1 : length(newGeneMat)
%    
%     geneMat = newGeneMat{i}; 
%     
%     for j = 1 : size(geneMat,3)
%         
%         if j == 1
%             G = geneMat(:,:,j);
%         else
%             G = [G geneMat(:,:,j)];
%         end
%         
%     end
%     
%     clear geneMat;
%     G = permute(G, [2 1 3]);
%     [RHO, PVAL] = corr(G, 'Type', 'Spearman');
%     clear G;
%     
%     save(['results\geneCorr\Concat\ageGroup' num2str(i) '_corrMat.mat'], 'RHO');
%     save(['results\geneCorr\Concat_pval\ageGroup' num2str(i) '_corrMat.mat'], 'PVAL');
%     clear RHO; clear PVAL;
%     
% end
%%%------------------------------------------------------------------------