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Mean filtering is used in HiCRep [30] as a preprocessing step to measure reproducibility of Hi-C datasets. To create a smoothed matrix Xs from a given input matrix X with a mean filter, each element in xijs is estimated from the mean of its neighboring elements within radius r: xijs=1(2r+1)2a=iri+rb=jrj+rxab. Three different values for the radius r were considered: r∈{3,6,11}.

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