# R script for Peak Model
#  -- generated by MACS
p <- c(0.0344284871139,0.0377073906486,0.0426257459506,0.0442651977179,0.0508230047872,0.0524624565545,0.0541019083219,0.0541019083219,0.0557413600892,0.0573808118565,0.0590202636238,0.0590202636238,0.0639386189258,0.0688569742278,0.0688569742278,0.0688569742278,0.0672175224605,0.0639386189258,0.0541019083219,0.0573808118565,0.0573808118565,0.0622991671585,0.0590202636238,0.0606597153912,0.0606597153912,0.0590202636238,0.0622991671585,0.0606597153912,0.0672175224605,0.0606597153912,0.0639386189258,0.0655780706932,0.0704964259951,0.0688569742278,0.0721358777625,0.0786936848318,0.0819725883665,0.0885303954358,0.0868909436684,0.0901698472031,0.0901698472031,0.0885303954358,0.0885303954358,0.0885303954358,0.0852514919011,0.0803331365991,0.0704964259951,0.0672175224605,0.0688569742278,0.0622991671585,0.0590202636238,0.0590202636238,0.0557413600892,0.0557413600892,0.0573808118565,0.0557413600892,0.0573808118565,0.0557413600892,0.0557413600892,0.0622991671585,0.0688569742278,0.0704964259951,0.0737753295298,0.0704964259951,0.0737753295298,0.0770542330645,0.0819725883665,0.0770542330645,0.0786936848318,0.0803331365991,0.0786936848318,0.0737753295298,0.0704964259951,0.0770542330645,0.0737753295298,0.0688569742278,0.0655780706932,0.0672175224605,0.0672175224605,0.0655780706932,0.0622991671585,0.0721358777625,0.0721358777625,0.0737753295298,0.0737753295298,0.0737753295298,0.0770542330645,0.0836120401338,0.0803331365991,0.0852514919011,0.0819725883665,0.0704964259951,0.0672175224605,0.0606597153912,0.0655780706932,0.0655780706932,0.0655780706932,0.0606597153912,0.0672175224605,0.0688569742278,0.0770542330645,0.0770542330645,0.0803331365991,0.0852514919011,0.0836120401338,0.0852514919011,0.0950882025051,0.100006557807,0.0983671060397,0.0918092989704,0.0852514919011,0.0918092989704,0.0918092989704,0.0885303954358,0.0803331365991,0.0803331365991,0.0655780706932,0.0606597153912,0.0557413600892,0.0573808118565,0.0622991671585,0.0557413600892,0.0573808118565,0.0541019083219,0.0606597153912,0.0639386189258,0.0688569742278,0.0721358777625,0.0754147812971,0.0704964259951,0.0622991671585,0.0606597153912,0.0590202636238,0.0606597153912,0.0573808118565,0.0541019083219,0.0573808118565,0.0573808118565,0.0573808118565,0.0639386189258,0.0737753295298,0.0754147812971,0.0721358777625,0.0721358777625,0.0770542330645,0.0803331365991,0.0737753295298,0.0786936848318,0.0852514919011,0.0852514919011,0.0852514919011,0.0885303954358,0.0918092989704,0.0868909436684,0.0885303954358,0.0901698472031,0.0967276542724,0.0885303954358,0.0786936848318,0.0770542330645,0.0721358777625,0.0819725883665,0.0803331365991,0.0885303954358,0.0770542330645,0.0754147812971,0.0721358777625,0.0721358777625,0.0737753295298,0.0737753295298,0.0754147812971,0.0655780706932,0.0672175224605,0.0590202636238,0.0655780706932,0.0754147812971,0.0704964259951,0.0688569742278,0.0639386189258,0.0606597153912,0.0606597153912,0.0573808118565,0.0541019083219,0.0655780706932,0.0688569742278,0.0557413600892,0.0721358777625,0.0786936848318,0.0852514919011,0.0836120401338,0.0803331365991,0.0901698472031,0.0967276542724,0.0901698472031,0.0819725883665,0.0770542330645,0.0622991671585,0.0557413600892,0.0557413600892,0.0639386189258,0.0688569742278,0.0639386189258,0.0590202636238,0.0606597153912,0.0622991671585,0.0704964259951,0.0803331365991,0.0901698472031,0.0934487507378,0.0934487507378,0.0868909436684,0.0836120401338,0.0819725883665,0.0803331365991,0.0868909436684,0.0868909436684,0.0803331365991,0.0770542330645,0.0721358777625,0.0655780706932,0.0688569742278,0.0721358777625,0.0737753295298,0.0786936848318,0.0754147812971,0.0721358777625,0.0704964259951,0.0672175224605,0.0672175224605,0.0737753295298,0.0836120401338,0.0803331365991,0.0836120401338,0.0770542330645,0.0754147812971,0.0737753295298,0.0770542330645,0.0754147812971,0.0688569742278,0.0622991671585,0.0524624565545,0.0541019083219,0.0491835530199,0.0557413600892,0.0524624565545,0.0622991671585,0.0590202636238,0.0655780706932,0.0737753295298,0.0786936848318,0.0819725883665,0.0868909436684,0.0885303954358,0.0868909436684,0.0852514919011,0.0803331365991,0.0803331365991,0.0770542330645,0.0721358777625,0.0672175224605,0.0639386189258,0.0606597153912,0.0688569742278,0.0672175224605,0.0786936848318,0.0770542330645,0.0836120401338,0.0819725883665,0.0868909436684,0.0967276542724,0.100006557807,0.101646009574,0.0950882025051,0.0934487507378,0.0918092989704,0.0934487507378,0.0901698472031,0.0934487507378,0.0852514919011,0.0737753295298,0.0704964259951,0.0639386189258,0.0672175224605,0.0688569742278,0.0672175224605,0.0688569742278,0.0737753295298,0.0688569742278,0.0754147812971,0.0737753295298,0.0754147812971,0.0836120401338,0.0786936848318,0.0770542330645,0.0770542330645,0.0737753295298,0.0688569742278,0.0721358777625,0.0737753295298,0.0803331365991,0.0754147812971,0.0737753295298,0.0819725883665,0.0885303954358,0.0934487507378,0.0885303954358,0.101646009574,0.106564364876,0.104924913109,0.104924913109,0.113122171946,0.108203816644,0.103285461342,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m <- 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ycorr <- 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altd  <- c(11, 41, 123, 128, 173, 197, 214, 266, 302, 337, 408, 501, 565, 587)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('55-MBD7-GSE58789/MBD7-5-Myc-ChIP-rep1-GSM1419608/all.1x36mers.TAIR10.unique.MACS2_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) : 11,41,123,128,173,197,214,266,302,337,408,501,565,587',bty='n')
dev.off()