is.broadpeak FALSE 
read /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-A549/A549-100nM-Dex-12h-DNAse-Rep1-ENCFF698TBJ/A549-100nM-Dex-12h-DNAse-Rep1-ENCFF698TBJ.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-12h-DNAse-Rep3-ENCFF204FPY/A549-100nM-Dex-12h-DNAse-Rep3-ENCFF204FPY.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-12h-DNAse-Rep1-vs-Rep3-uri.sav 
EM is done

EM is saved at: A549-100nM-Dex-12h-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-12h-DNAse-Rep1-ENCFF698TBJ/A549-100nM-Dex-12h-DNAse-Rep1-ENCFF698TBJ.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-12h-DNAse-Rep3-ENCFF204FPY/A549-100nM-Dex-12h-DNAse-Rep3-ENCFF204FPY.hg20-male.20mers.unique.MACS-2.1.0.p1e-1.narrowPeak.top100K-p-value-sort
$p
[1] 0.6938262

$rho1
[1] 0.9086162

$rho2
[1] 0

Write overlapped peaks and local idr to: A549-100nM-Dex-12h-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] 23462.83

$x.mean2
[1] 47433.37

$y.mean1
[1] 23703.76

$y.mean2
[1] 46888.2

$x.sd1
[1] 15360.71

$x.sd2
[1] 9982.574

$y.sd1
[1] 15634.8

$y.sd2
[1] 10302.22