# R script for Peak Model
#  -- generated by MACS
p <- c(0.0421696790201,0.0500152006983,0.0549186517471,0.0657062440546,0.0696290048936,0.072571075523,0.0715903853132,0.0686483146839,0.0676676244741,0.076493836362,0.0813972874109,0.0813972874109,0.08532004825,0.0813972874109,0.0863007384597,0.089242809089,0.0921848797183,0.098069020977,0.0990497111867,0.0941462601379,0.0882621188793,0.0912041895086,0.0951269503477,0.102972472026,0.101011091606,0.0951269503477,0.0931655699281,0.0990497111867,0.098069020977,0.0970883307672,0.0961076405574,0.0912041895086,0.0863007384597,0.0804165972011,0.0774745265718,0.0804165972011,0.0784552167816,0.0696290048936,0.0686483146839,0.0686483146839,0.0706096951034,0.0706096951034,0.0715903853132,0.0745324559425,0.076493836362,0.08532004825,0.0863007384597,0.0931655699281,0.0951269503477,0.0951269503477,0.0961076405574,0.0961076405574,0.0941462601379,0.0931655699281,0.0951269503477,0.0833586678304,0.0833586678304,0.0745324559425,0.0774745265718,0.0774745265718,0.072571075523,0.072571075523,0.0735517657327,0.072571075523,0.0686483146839,0.0696290048936,0.0696290048936,0.0755131461523,0.0696290048936,0.0686483146839,0.0715903853132,0.0706096951034,0.0735517657327,0.0706096951034,0.0745324559425,0.0755131461523,0.0774745265718,0.0755131461523,0.0794359069913,0.0794359069913,0.0784552167816,0.0774745265718,0.072571075523,0.076493836362,0.076493836362,0.076493836362,0.0774745265718,0.0755131461523,0.076493836362,0.0813972874109,0.0794359069913,0.0833586678304,0.0872814286695,0.0823779776206,0.0794359069913,0.0813972874109,0.0794359069913,0.0774745265718,0.0745324559425,0.0706096951034,0.076493836362,0.072571075523,0.0657062440546,0.0666869342643,0.0666869342643,0.0627641734253,0.0608027930057,0.0578607223764,0.0549186517471,0.0529572713276,0.0470731300689,0.0519765811178,0.0549186517471,0.0558993419569,0.0558993419569,0.0558993419569,0.0568800321666,0.0608027930057,0.0666869342643,0.0696290048936,0.0706096951034,0.0666869342643,0.0686483146839,0.0676676244741,0.0676676244741,0.0696290048936,0.072571075523,0.0696290048936,0.0647255538448,0.0686483146839,0.0706096951034,0.0735517657327,0.0715903853132,0.0706096951034,0.0735517657327,0.0706096951034,0.0696290048936,0.0696290048936,0.0715903853132,0.0745324559425,0.0715903853132,0.0696290048936,0.072571075523,0.076493836362,0.076493836362,0.0774745265718,0.0755131461523,0.0833586678304,0.0794359069913,0.0735517657327,0.0774745265718,0.0794359069913,0.0774745265718,0.072571075523,0.072571075523,0.0745324559425,0.0755131461523,0.0755131461523,0.0843393580402,0.0843393580402,0.08532004825,0.0882621188793,0.0941462601379,0.101991781816,0.0990497111867,0.101991781816,0.0970883307672,0.0970883307672,0.0921848797183,0.0912041895086,0.089242809089,0.0872814286695,0.0843393580402,0.0794359069913,0.0804165972011,0.0755131461523,0.0755131461523,0.072571075523,0.0745324559425,0.0774745265718,0.0735517657327,0.0706096951034,0.072571075523,0.076493836362,0.0794359069913,0.0794359069913,0.0902234992988,0.0882621188793,0.0813972874109,0.0755131461523,0.0784552167816,0.0813972874109,0.0823779776206,0.0823779776206,0.0784552167816,0.0804165972011,0.0706096951034,0.072571075523,0.076493836362,0.0794359069913,0.076493836362,0.076493836362,0.0696290048936,0.0657062440546,0.0715903853132,0.0686483146839,0.0735517657327,0.0735517657327,0.0755131461523,0.0735517657327,0.0755131461523,0.0735517657327,0.0755131461523,0.0715903853132,0.0686483146839,0.0715903853132,0.0657062440546,0.0647255538448,0.0627641734253,0.0617834832155,0.0627641734253,0.0676676244741,0.0676676244741,0.0657062440546,0.0647255538448,0.063744863635,0.0696290048936,0.0706096951034,0.0745324559425,0.0755131461523,0.0784552167816,0.0745324559425,0.0735517657327,0.0774745265718,0.0745324559425,0.0784552167816,0.0715903853132,0.072571075523,0.0676676244741,0.0696290048936,0.0657062440546,0.0627641734253,0.0598221027959,0.0617834832155,0.0608027930057,0.0598221027959,0.0647255538448,0.0598221027959,0.0647255538448,0.0617834832155,0.0588414125862,0.0558993419569,0.063744863635,0.0657062440546,0.0706096951034,0.0715903853132,0.0735517657327,0.0794359069913,0.0813972874109,0.089242809089,0.098069020977,0.100030401397,0.0961076405574,0.0931655699281,0.0951269503477,0.089242809089,0.0872814286695,0.0823779776206,0.0794359069913,0.0715903853132,0.0666869342643,0.0735517657327,0.0755131461523,0.0804165972011,0.0735517657327,0.0813972874109,0.0794359069913,0.0784552167816,0.076493836362,0.0794359069913,0.0833586678304,0.0804165972011,0.0755131461523,0.0706096951034,0.076493836362,0.0706096951034,0.072571075523,0.0804165972011,0.0813972874109,0.0863007384597,0.0823779776206,0.0823779776206,0.0823779776206,0.0833586678304,0.0823779776206,0.0813972874109,0.0804165972011,0.0794359069913,0.076493836362,0.0745324559425,0.0735517657327,0.0696290048936,0.0676676244741,0.0657062440546,0.063744863635,0.0598221027959,0.0608027930057,0.0549186517471,0.0578607223764,0.0608027930057,0.0588414125862,0.0617834832155,0.0657062440546,0.0666869342643,0.072571075523,0.083358667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m <- 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ycorr <- 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altd  <- c(36, 96, 197, 255, 362, 435, 494, 529, 546)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('33-SEP3-AP1-24581456/SEP3-ChIP-seq-2d-biological-replicate-2-GSM1279839/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) : 36,96,197,255,362,435,494,529,546',bty='n')
dev.off()