is.broadpeak FALSE 
[1] "Fix 1 stops\n"
read /woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-A549/A549-100nM-Dex-2h-DNAse-Rep1-ENCFF612IFF/A549-100nM-Dex-2h-DNAse-Rep1-ENCFF612IFF.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-2h-DNAse-Rep2-ENCFF261DOR/A549-100nM-Dex-2h-DNAse-Rep2-ENCFF261DOR.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-2h-DNAse-Rep1-vs-Rep2-uri.sav 
EM is done

EM is saved at: A549-100nM-Dex-2h-DNAse-Rep1-vs-Rep2-em.sav 
EM estimation for the following files
/woldlab/castor/home/georgi/papers/2017-ENCODE-enhancers/datasets-A549/A549-100nM-Dex-2h-DNAse-Rep1-ENCFF612IFF/A549-100nM-Dex-2h-DNAse-Rep1-ENCFF612IFF.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-2h-DNAse-Rep2-ENCFF261DOR/A549-100nM-Dex-2h-DNAse-Rep2-ENCFF261DOR.hg20-male.20mers.unique.MACS-2.1.0.p1e-1.narrowPeak.top100K-p-value-sort
$p
[1] 0.6833486

$rho1
[1] 0.8935308

$rho2
[1] 0

Write overlapped peaks and local idr to: A549-100nM-Dex-2h-DNAse-Rep1-vs-Rep2-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] 22775.7

$x.mean2
[1] 44497.09

$y.mean1
[1] 22609.7

$y.mean2
[1] 44854.82

$x.sd1
[1] 15145.49

$x.sd2
[1] 10407.05

$y.sd1
[1] 15042.59

$y.sd2
[1] 9963.551