is.broadpeak FALSE 
read K562-DNAse-Rep1-UW.hg20-female.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort :  100000 peaks
 100000 peaks are left after cleaning
 K562-DNAse-Rep2-UW.hg20-female.36mers.unique.MACS-2.1.0.p1e-1_peaks.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: K562-DNAse-UW-Rep1-vs-Rep2-uri.sav 
EM is done

EM is saved at: K562-DNAse-UW-Rep1-vs-Rep2-em.sav 
EM estimation for the following files
K562-DNAse-Rep1-UW.hg20-female.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort
K562-DNAse-Rep2-UW.hg20-female.36mers.unique.MACS-2.1.0.p1e-1_peaks.narrowPeak.top100K-p-value-sort
$p
[1] 0.6638454

$rho1
[1] 0.9590424

$rho2
[1] 0

Write overlapped peaks and local idr to: K562-DNAse-UW-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] 30344.18

$x.mean2
[1] 64321.64

$y.mean1
[1] 30370.75

$y.mean2
[1] 64269.2

$x.sd1
[1] 20162.36

$x.sd2
[1] 12666.98

$y.sd1
[1] 20270.66

$y.sd2
[1] 12464.81