is.broadpeak FALSE 
read /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-A549/A549-100nM-Dex-6h-DNAse-Rep2-ENCFF182HDJ/A549-100nM-Dex-6h-DNAse-Rep2-ENCFF182HDJ.hg20-male.20mers.unique.MACS-2.1.0.p1e-1.narrowPeak.top100K-p-value-sort :  100000 peaks
 100000 peaks are left after cleaning
 /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-A549/A549-100nM-Dex-6h-DNAse-Rep3-ENCFF692PJP/A549-100nM-Dex-6h-DNAse-Rep3-ENCFF692PJP.hg20-male.20mers.unique.MACS-2.1.0.p1e-1.narrowPeak.top100K-p-value-sort :  100000 peaks
 100000  peaks are left after cleaninghalf.width= reported 
significant measure= p.value 
URI is done
URI is saved at: A549-100nM-Dex-6h-DNAse-Rep2-vs-Rep3-uri.sav 
EM is done

EM is saved at: A549-100nM-Dex-6h-DNAse-Rep2-vs-Rep3-em.sav 
EM estimation for the following files
/woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-A549/A549-100nM-Dex-6h-DNAse-Rep2-ENCFF182HDJ/A549-100nM-Dex-6h-DNAse-Rep2-ENCFF182HDJ.hg20-male.20mers.unique.MACS-2.1.0.p1e-1.narrowPeak.top100K-p-value-sort
/woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-A549/A549-100nM-Dex-6h-DNAse-Rep3-ENCFF692PJP/A549-100nM-Dex-6h-DNAse-Rep3-ENCFF692PJP.hg20-male.20mers.unique.MACS-2.1.0.p1e-1.narrowPeak.top100K-p-value-sort
$p
[1] 0.668854

$rho1
[1] 0.8881044

$rho2
[1] 0

Write overlapped peaks and local idr to: A549-100nM-Dex-6h-DNAse-Rep2-vs-Rep3-overlapped-peaks.txt
Write number of peaks above IDR cutoff [0.01, 0.25]: npeaks-aboveIDR.txt
Marginal mean of two components:
$x.mean1
[1] 21560.24

$x.mean2
[1] 43359.89

$y.mean1
[1] 21748.62

$y.mean2
[1] 42979.9

$x.sd1
[1] 14348.8

$x.sd2
[1] 10002.63

$y.sd1
[1] 14612.84

$y.sd2
[1] 10048.81