%MATLAB code for calculating the autocorrelation function of transcription factor alpha-coefficients

N = 36;  %The number of time points

pstrengths = zeros(length(TFList),1);
autoCorrFn = zeros(length(TFList),N);
RxxRange = [1 2*N-1];

%Find autocorrelation for each TF in TFList, which contains top 20 TFs
for k = 1:length(TFList)
    [Rxx, lag]=xcorr(alphaCoeffs(k+1,:));
    startCoord = round(RxxRange(2)/2);
    endCoord = RxxRange(2);

    %Ignore the first few values, because those will have high 
    %autocorrelation no matter what.
    [a,delay]=max(abs(Rxx(1:N-6)));

    %We expect to see a peak at Rxx(24). Normalize this value.
    autoCorrFn(k,:)=Rxx(startCoord:endCoord);
    periodic_strength = Rxx(24)/autoCorrFn(k,1);

    %Store the periodicity score for the kth TF in pstrengths
    pstrengths(k) = periodic_strength;
end