# R script for Peak Model
#  -- generated by MACS
p <- c(0.0393298501995,0.0458848252328,0.0543677340994,0.0609227091326,0.0674776841659,0.0632362297326,0.0659353370992,0.0643929900326,0.0636218164993,0.0624650561993,0.0647785767992,0.0620794694326,0.0597659488326,0.0562956679327,0.0562956679327,0.0574524282327,0.054753320866,0.0562956679327,0.0532109737994,0.0562956679327,0.057066841466,0.0586091885326,0.0586091885326,0.0643929900326,0.0636218164993,0.0620794694326,0.0636218164993,0.0620794694326,0.0647785767992,0.0628506429659,0.0636218164993,0.0670920973992,0.0659353370992,0.0651641635659,0.0678632709325,0.0686344444659,0.0686344444659,0.0701767915325,0.0694056179992,0.0694056179992,0.0667065106326,0.0632362297326,0.0636218164993,0.0601515355993,0.0597659488326,0.0609227091326,0.0616938826659,0.0632362297326,0.0643929900326,0.0632362297326,0.0632362297326,0.0640074032659,0.0640074032659,0.0640074032659,0.0628506429659,0.0620794694326,0.060537122366,0.0601515355993,0.0601515355993,0.0616938826659,0.0616938826659,0.0613082958993,0.059380362066,0.0643929900326,0.0647785767992,0.0659353370992,0.0663209238659,0.0678632709325,0.0663209238659,0.0651641635659,0.0640074032659,0.0632362297326,0.0651641635659,0.0632362297326,0.060537122366,0.058223601766,0.0597659488326,0.0586091885326,0.0586091885326,0.0597659488326,0.0632362297326,0.0624650561993,0.0647785767992,0.0624650561993,0.0601515355993,0.059380362066,0.0574524282327,0.0574524282327,0.0586091885326,0.0574524282327,0.0566812546993,0.0578380149993,0.0555244943994,0.058223601766,0.060537122366,0.0616938826659,0.0651641635659,0.0640074032659,0.0640074032659,0.0636218164993,0.0632362297326,0.0632362297326,0.0667065106326,0.0663209238659,0.0686344444659,0.0678632709325,0.0632362297326,0.0616938826659,0.0613082958993,0.0632362297326,0.0636218164993,0.0659353370992,0.0628506429659,0.0624650561993,0.0613082958993,0.0628506429659,0.0632362297326,0.0628506429659,0.0643929900326,0.0636218164993,0.0647785767992,0.0640074032659,0.0651641635659,0.0655497503326,0.0651641635659,0.0670920973992,0.0690200312325,0.0701767915325,0.0674776841659,0.0690200312325,0.0682488576992,0.0670920973992,0.0655497503326,0.0659353370992,0.0670920973992,0.0678632709325,0.0694056179992,0.0694056179992,0.0713335518325,0.0705623782992,0.0694056179992,0.0732614856658,0.0763461797991,0.0751894194991,0.0755750062658,0.0740326591991,0.0701767915325,0.0724903121325,0.0713335518325,0.0694056179992,0.0717191385992,0.0690200312325,0.0663209238659,0.0651641635659,0.0628506429659,0.060537122366,0.0620794694326,0.0597659488326,0.0597659488326,0.0609227091326,0.060537122366,0.0597659488326,0.059380362066,0.0589947752993,0.060537122366,0.0628506429659,0.0632362297326,0.0636218164993,0.0674776841659,0.0670920973992,0.0647785767992,0.0659353370992,0.0701767915325,0.0724903121325,0.0705623782992,0.0694056179992,0.0674776841659,0.0690200312325,0.0643929900326,0.0647785767992,0.0643929900326,0.0632362297326,0.0609227091326,0.0589947752993,0.060537122366,0.0616938826659,0.0620794694326,0.0613082958993,0.0609227091326,0.060537122366,0.0616938826659,0.0640074032659,0.0636218164993,0.0647785767992,0.0651641635659,0.0647785767992,0.0678632709325,0.0659353370992,0.0697912047659,0.0690200312325,0.0690200312325,0.0717191385992,0.0713335518325,0.0709479650658,0.0717191385992,0.0724903121325,0.0705623782992,0.0713335518325,0.0713335518325,0.0736470724325,0.0751894194991,0.0709479650658,0.0694056179992,0.0682488576992,0.0678632709325,0.0659353370992,0.0632362297326,0.0628506429659,0.0586091885326,0.0555244943994,0.0562956679327,0.055910081166,0.0562956679327,0.0578380149993,0.0555244943994,0.0562956679327,0.0601515355993,0.0632362297326,0.0674776841659,0.0686344444659,0.0636218164993,0.0620794694326,0.0624650561993,0.0624650561993,0.0647785767992,0.0620794694326,0.059380362066,0.055910081166,0.053596560566,0.053596560566,0.054753320866,0.0555244943994,0.0562956679327,0.054753320866,0.0539821473327,0.055910081166,0.0551389076327,0.057066841466,0.0589947752993,0.060537122366,0.060537122366,0.0601515355993,0.0601515355993,0.0609227091326,0.060537122366,0.0632362297326,0.0640074032659,0.0667065106326,0.0651641635659,0.0651641635659,0.0670920973992,0.0701767915325,0.0686344444659,0.0694056179992,0.0686344444659,0.0667065106326,0.0697912047659,0.0674776841659,0.0682488576992,0.0682488576992,0.0713335518325,0.0709479650658,0.0751894194991,0.0778885268658,0.0817443945324,0.0825155680657,0.0802020474657,0.0778885268658,0.0778885268658,0.0767317665658,0.0732614856658,0.0740326591991,0.0736470724325,0.0674776841659,0.0709479650658,0.0728758988991,0.0744182459658,0.0778885268658,0.0763461797991,0.0790452871657,0.0798164606991,0.0786597003991,0.0771173533324,0.082129981299,0.0798164606991,0.0767317665658,0.0744182459658,0.0717191385992,0.0740326591991,0.0740326591991,0.0740326591991,0.0709479650658,0.0697912047659,0.0686344444659,0.0670920973992,0.0682488576992,0.0713335518325,0.0744182459658,0.0740326591991,0.0709479650658,0.0717191385992,0.0763461797991,0.0771173533324,0.0771173533324,0.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m <- 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ycorr <- 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xcorr <- 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altd  <- c(36, 249, 276, 388, 418, 479, 500, 587)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('13-REV-GSE26722/rev-GSM657970/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) : 36,249,276,388,418,479,500,587',bty='n')
dev.off()