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twoGenesCorr.m
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twoGenesCorr.m
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%%% 15 Feb. 2013
%%% calculate the correlation between two genes within a
%%% specific structure (defined by the ABA acronym)
% define the files directory
filesDirectory = 'files/';
matObj = matfile([filesDirectory 'fullExpressionMatrix.mat']);
% load gene names
load([filesDirectory 'allGenes.mat']);
% load experiments' numbers
load([filesDirectory 'allExpNumbers.mat']);
% load voxels annotations
load([filesDirectory 'voxelAnnotation.mat']);
geneA = 'Tph2';
geneB = 'Maob';
strOfInterest = 'MB';
geneA_index = find(strcmp(allGenes, geneA) == 1);
geneA_experimentNo = allExpNumbers(geneA_index);
geneB_index = find(ismember(allGenes, geneB) == 1);
geneB_experimentNo = allExpNumbers(geneB_index);
indx = [geneA_index geneB_index];
for i = 1 : length(indx)
if i == 1
miniExpMat = matObj.fullExpressionMatrix(:,indx(i));
else
miniExpMat = [miniExpMat matObj.fullExpressionMatrix(:,indx(i))];
end
end
inclVoxAnnotations = indicateSubStr(strOfInterest, 'files/');
inclVoxelsInd = find(ismember(voxelAnnotation, inclVoxAnnotations) == 1);
expMat_logTransformed = miniExpMat;
dataMat = expMat_logTransformed(inclVoxelsInd, :);
c = corr(dataMat, 'type', 'Spearman');