is.broadpeak FALSE 
read /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-A549/A549-100nM-Dex-6h-DNAse-Rep1-ENCFF211UDW/A549-100nM-Dex-6h-DNAse-Rep1-ENCFF211UDW.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-Rep1-vs-Rep3-uri.sav 
EM is done

EM is saved at: A549-100nM-Dex-6h-DNAse-Rep1-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-Rep1-ENCFF211UDW/A549-100nM-Dex-6h-DNAse-Rep1-ENCFF211UDW.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] 0.7007276

$rho1
[1] 0.9005865

$rho2
[1] 0

Write overlapped peaks and local idr to: A549-100nM-Dex-6h-DNAse-Rep1-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] 23485.04

$x.mean2
[1] 45991.3

$y.mean1
[1] 23469.26

$y.mean2
[1] 46028.19

$x.sd1
[1] 15436.62

$x.sd2
[1] 10219.63

$y.sd1
[1] 15417.23

$y.sd2
[1] 10206.73