# R script for Peak Model
#  -- generated by MACS
p <- c(0.0446075993799,0.0511890484687,0.0621581302834,0.0716646678562,0.0775148448241,0.0738584842191,0.0745897563401,0.078977389066,0.078977389066,0.0775148448241,0.079708661187,0.0833650217919,0.0840962939129,0.0833650217919,0.0862901102758,0.0884839266388,0.0899464708807,0.0870213823968,0.0877526545178,0.0884839266388,0.0877526545178,0.0877526545178,0.078977389066,0.0745897563401,0.0702021236142,0.0702021236142,0.0687395793723,0.0628894024044,0.0577704975576,0.0592330417995,0.0585017696785,0.0577704975576,0.0606955860415,0.0614268581625,0.0643519466464,0.0614268581625,0.0614268581625,0.0643519466464,0.0658144908883,0.0621581302834,0.0614268581625,0.0606955860415,0.0621581302834,0.0636206745254,0.0628894024044,0.0628894024044,0.0599643139205,0.0570392254366,0.0555766811946,0.0548454090736,0.0555766811946,0.0555766811946,0.0548454090736,0.0555766811946,0.0533828648317,0.0541141369526,0.0548454090736,0.0577704975576,0.0614268581625,0.0658144908883,0.0687395793723,0.0665457630093,0.0665457630093,0.0672770351303,0.0694708514933,0.0694708514933,0.0694708514933,0.0672770351303,0.0665457630093,0.0650832187674,0.0592330417995,0.0577704975576,0.0614268581625,0.0592330417995,0.0628894024044,0.0650832187674,0.0636206745254,0.0658144908883,0.0680083072513,0.0672770351303,0.0709333957352,0.0723959399772,0.0672770351303,0.0694708514933,0.0672770351303,0.0650832187674,0.0672770351303,0.0702021236142,0.0694708514933,0.0694708514933,0.0709333957352,0.0716646678562,0.0702021236142,0.0672770351303,0.0658144908883,0.0658144908883,0.0658144908883,0.0585017696785,0.0555766811946,0.0541141369526,0.0541141369526,0.0541141369526,0.0541141369526,0.0533828648317,0.0533828648317,0.0497265042268,0.0475326878638,0.0504577763477,0.0519203205897,0.0519203205897,0.0460701436218,0.0438763272589,0.0468014157428,0.0482639599848,0.0460701436218,0.0482639599848,0.0519203205897,0.0504577763477,0.0475326878638,0.0482639599848,0.0519203205897,0.0526515927107,0.0519203205897,0.0497265042268,0.0489952321058,0.0519203205897,0.0497265042268,0.0533828648317,0.0570392254366,0.0606955860415,0.0592330417995,0.0606955860415,0.0643519466464,0.0709333957352,0.0702021236142,0.0716646678562,0.0702021236142,0.0672770351303,0.0643519466464,0.0614268581625,0.0621581302834,0.0628894024044,0.0570392254366,0.0511890484687,0.0533828648317,0.0526515927107,0.0563079533156,0.0541141369526,0.0599643139205,0.0636206745254,0.0628894024044,0.0606955860415,0.0628894024044,0.0672770351303,0.0716646678562,0.0738584842191,0.0767835727031,0.080439933308,0.0760523005821,0.0738584842191,0.078246116945,0.078246116945,0.078246116945,0.080439933308,0.080439933308,0.079708661187,0.078246116945,0.0775148448241,0.079708661187,0.079708661187,0.078977389066,0.0848275660339,0.0892151987598,0.0855588381549,0.0826337496709,0.081171205429,0.081171205429,0.0833650217919,0.0819024775499,0.0833650217919,0.078977389066,0.0753210284611,0.0709333957352,0.0694708514933,0.0672770351303,0.0665457630093,0.0643519466464,0.0606955860415,0.0614268581625,0.0628894024044,0.0650832187674,0.0643519466464,0.0628894024044,0.0614268581625,0.0636206745254,0.0643519466464,0.0680083072513,0.0716646678562,0.0753210284611,0.0753210284611,0.0731272120982,0.0723959399772,0.0753210284611,0.078246116945,0.079708661187,0.0767835727031,0.0760523005821,0.0745897563401,0.0716646678562,0.0709333957352,0.0716646678562,0.0709333957352,0.0687395793723,0.0687395793723,0.0680083072513,0.0709333957352,0.0680083072513,0.0650832187674,0.0665457630093,0.0606955860415,0.0621581302834,0.0636206745254,0.0650832187674,0.0621581302834,0.0636206745254,0.0577704975576,0.0555766811946,0.0570392254366,0.0511890484687,0.0548454090736,0.0519203205897,0.0468014157428,0.0460701436218,0.0475326878638,0.0446075993799,0.0489952321058,0.0511890484687,0.0526515927107,0.0563079533156,0.0555766811946,0.0570392254366,0.0606955860415,0.0599643139205,0.0636206745254,0.0650832187674,0.0643519466464,0.0621581302834,0.0621581302834,0.0672770351303,0.0643519466464,0.0643519466464,0.0628894024044,0.0658144908883,0.0621581302834,0.0621581302834,0.0636206745254,0.0643519466464,0.0599643139205,0.0526515927107,0.0533828648317,0.0548454090736,0.0577704975576,0.0563079533156,0.0585017696785,0.0621581302834,0.0628894024044,0.0628894024044,0.0680083072513,0.0738584842191,0.0745897563401,0.0731272120982,0.0709333957352,0.0745897563401,0.0738584842191,0.0694708514933,0.0709333957352,0.0723959399772,0.0680083072513,0.0658144908883,0.0636206745254,0.0606955860415,0.0606955860415,0.0563079533156,0.0533828648317,0.0526515927107,0.0541141369526,0.0563079533156,0.0606955860415,0.0599643139205,0.0658144908883,0.0687395793723,0.0723959399772,0.0731272120982,0.079708661187,0.080439933308,0.078977389066,0.0819024775499,0.0819024775499,0.0840962939129,0.0884839266388,0.0943341036066,0.0957966478486,0.100184280574,0.103840641179,0.107497001784,0.110422090268,0.111153362389,0.116272267236,0.112615906631,0.109690818147,0.107497001784,0.109690818147,0.114078450873,0.107497001784,0.1053031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m <- 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ycorr <- 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altd  <- c(37, 118, 164, 191, 246, 298, 418, 451, 530, 561)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('45-AL5-GSE56706/AL5_OE-GSM1367107/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) : 37,118,164,191,246,298,418,451,530,561',bty='n')
dev.off()