# R script for Peak Model
#  -- generated by MACS
p <- c(0.0400822349429,0.046187476027,0.0529563302723,0.0602560750467,0.0679539877178,0.0679539877178,0.0684848782469,0.0672903745565,0.0690157687759,0.0691484914082,0.0690157687759,0.0699448272018,0.0692812140405,0.0686176008792,0.0667594840275,0.0666267613952,0.0652995350726,0.0663613161307,0.0649013671758,0.0652995350726,0.0643704766468,0.0638395861177,0.0643704766468,0.0651668124404,0.0650340898081,0.0650340898081,0.067024929292,0.0682194329824,0.0686176008792,0.0683521556146,0.0696793819372,0.0692812140405,0.0691484914082,0.0692812140405,0.070077549834,0.0691484914082,0.0688830461437,0.0671576519243,0.0679539877178,0.0662285934984,0.0651668124404,0.0656977029694,0.0652995350726,0.0656977029694,0.0647686445436,0.0658304256017,0.0652995350726,0.0663613161307,0.0662285934984,0.0687503235114,0.070077549834,0.0699448272018,0.0704757177308,0.0698121045695,0.072068389318,0.0727320024793,0.0728647251115,0.072068389318,0.072068389318,0.0707411629953,0.070077549834,0.0704757177308,0.0719356666857,0.0698121045695,0.0687503235114,0.067024929292,0.067024929292,0.0666267613952,0.0658304256017,0.0660958708662,0.0660958708662,0.0662285934984,0.063441418221,0.0641050313823,0.0629105276919,0.0641050313823,0.0635741408532,0.0642377540145,0.0647686445436,0.0631759729564,0.0635741408532,0.0638395861177,0.0651668124404,0.0663613161307,0.0672903745565,0.0662285934984,0.067024929292,0.0668922066598,0.0678212650856,0.0687503235114,0.0687503235114,0.0672903745565,0.0676885424533,0.0680867103501,0.0680867103501,0.0687503235114,0.0684848782469,0.0691484914082,0.0686176008792,0.0683521556146,0.0684848782469,0.0699448272018,0.0707411629953,0.0702102724663,0.0694139366727,0.0686176008792,0.0671576519243,0.0659631482339,0.066494038763,0.0671576519243,0.0667594840275,0.0666267613952,0.0658304256017,0.0652995350726,0.0662285934984,0.0671576519243,0.0674230971888,0.0679539877178,0.0666267613952,0.0671576519243,0.0663613161307,0.0671576519243,0.0668922066598,0.067024929292,0.0659631482339,0.0652995350726,0.0671576519243,0.0667594840275,0.0675558198211,0.0671576519243,0.0686176008792,0.0668922066598,0.0684848782469,0.0683521556146,0.0687503235114,0.0684848782469,0.0671576519243,0.0682194329824,0.0682194329824,0.0678212650856,0.0671576519243,0.0688830461437,0.0668922066598,0.0676885424533,0.0676885424533,0.0680867103501,0.0680867103501,0.0667594840275,0.0675558198211,0.0678212650856,0.0667594840275,0.0654322577049,0.0655649803371,0.0650340898081,0.0662285934984,0.0668922066598,0.066494038763,0.0667594840275,0.0658304256017,0.0667594840275,0.0662285934984,0.0655649803371,0.0651668124404,0.0655649803371,0.0663613161307,0.0662285934984,0.0651668124404,0.0654322577049,0.0654322577049,0.0646359219113,0.0652995350726,0.0656977029694,0.0660958708662,0.0654322577049,0.0649013671758,0.0637068634855,0.0642377540145,0.0637068634855,0.0625123597951,0.0621141918983,0.0623796371629,0.0626450824274,0.0631759729564,0.0622469145306,0.0605215203112,0.061450578737,0.0633086955887,0.0646359219113,0.0649013671758,0.0650340898081,0.0656977029694,0.0651668124404,0.0651668124404,0.0662285934984,0.066494038763,0.0659631482339,0.0651668124404,0.0631759729564,0.0646359219113,0.0658304256017,0.0652995350726,0.0652995350726,0.0655649803371,0.0667594840275,0.0672903745565,0.067024929292,0.0662285934984,0.0671576519243,0.0672903745565,0.0678212650856,0.070077549834,0.0704757177308,0.0711393308921,0.0703429950986,0.0702102724663,0.0711393308921,0.0711393308921,0.0724665572147,0.072068389318,0.0706084403631,0.0682194329824,0.0686176008792,0.0662285934984,0.0651668124404,0.0652995350726,0.0649013671758,0.0662285934984,0.0647686445436,0.0654322577049,0.0658304256017,0.0671576519243,0.0678212650856,0.0692812140405,0.069546659305,0.0706084403631,0.0719356666857,0.0722011119502,0.0723338345825,0.0719356666857,0.072599279847,0.0723338345825,0.0722011119502,0.0718029440534,0.073130170376,0.0727320024793,0.0723338345825,0.0729974477438,0.0733956156406,0.0722011119502,0.0711393308921,0.0710066082599,0.0702102724663,0.0715374987889,0.0710066082599,0.0704757177308,0.0710066082599,0.0702102724663,0.0694139366727,0.0704757177308,0.0710066082599,0.0704757177308,0.0714047761566,0.0706084403631,0.0714047761566,0.0718029440534,0.0706084403631,0.0698121045695,0.072068389318,0.0724665572147,0.072599279847,0.0728647251115,0.0735283382728,0.0733956156406,0.0735283382728,0.0745901193309,0.0755191777567,0.0765809588148,0.0760500682858,0.075651900389,0.0744573966987,0.0737937835374,0.0712720535244,0.0708738856276,0.0703429950986,0.0702102724663,0.0698121045695,0.0686176008792,0.0688830461437,0.0683521556146,0.0690157687759,0.0710066082599,0.0714047761566,0.0710066082599,0.0716702214212,0.0718029440534,0.0718029440534,0.0722011119502,0.0723338345825,0.0729974477438,0.0716702214212,0.0719356666857,0.0736610609051,0.0735283382728,0.0741919514341,0.0732628930083,0.0727320024793,0.0728647251115,0.0740592288019,0.0743246740664,0.0772445719761,0.0761827909181,0.0752537324922,0.0775100172407,0.0763155135503,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m <- 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ycorr <- 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altd  <- c(153)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('msl2_3-GSM929150.36mers.unique.MACS-2.1.0_model.pdf',height=6,width=6)
plot(x,p,type='l',col=c('red'),main='Peak Model',xlab='Distance to the middle',ylab='Percentage')
lines(x,m,col=c('blue'))
legend('topleft',c('forward tags','reverse tags'),lty=c(1,1,1),col=c('red','blue'))
plot(xcorr,ycorr,type='l',col=c('black'),main='Cross-Correlation',xlab='Lag between + and - tags',ylab='Correlation')
abline(v=altd,lty=2,col=c('red'))
legend('topleft','alternative lag(s)',lty=2,col='red')
legend('right','alt lag(s) : 153',bty='n')
dev.off()