# R script for Peak Model
#  -- generated by MACS
p <- c(0.0483267994153,0.0566568941181,0.0644357325537,0.0723983230784,0.080330288255,0.0805752910403,0.0807896684775,0.0803609136031,0.0801159108178,0.0799627840769,0.080330288255,0.0801465361659,0.0800852854696,0.0804834149958,0.0804527896477,0.0802077868623,0.0800240347732,0.0804221642995,0.0807590431294,0.0808509191739,0.0807590431294,0.080514040344,0.0807284177812,0.0802690375586,0.0800852854696,0.0806059163885,0.0806059163885,0.080514040344,0.0804834149958,0.0806365417367,0.0808202938257,0.0808815445221,0.0811571726556,0.0814328007892,0.0818309303154,0.0816165528782,0.0821678091453,0.0821984344935,0.0818003049672,0.0815246768337,0.0810959219593,0.0812796740483,0.0810040459147,0.0807896684775,0.0808509191739,0.0809121698702,0.0806365417367,0.0803609136031,0.0804527896477,0.0808202938257,0.0808509191739,0.0805446656922,0.0805752910403,0.0807590431294,0.0807590431294,0.0805446656922,0.0802996629068,0.0800852854696,0.0801465361659,0.0799015333806,0.0799015333806,0.0800546601214,0.0799627840769,0.0797790319879,0.0795646545507,0.0795340292025,0.0799015333806,0.0804527896477,0.0803609136031,0.0801771615141,0.0802384122104,0.0800240347732,0.0800852854696,0.0800240347732,0.0802996629068,0.0801465361659,0.0793502771135,0.0790746489799,0.0789521475872,0.0790133982836,0.0792584010689,0.0790440236317,0.0794727785062,0.0791052743281,0.0786152687573,0.0789827729354,0.0793809024616,0.0799321587287,0.0801771615141,0.0799934094251,0.079809657336,0.0799627840769,0.0797790319879,0.0801465361659,0.0803915389513,0.0801465361659,0.0802996629068,0.0798709080324,0.0801771615141,0.0806059163885,0.0804527896477,0.0809427952184,0.0808202938257,0.0810040459147,0.0808815445221,0.0808815445221,0.0811571726556,0.0811877980038,0.080697792433,0.0804834149958,0.0806059163885,0.0804527896477,0.0806059163885,0.0806059163885,0.0810040459147,0.0811877980038,0.0810346712629,0.0811571726556,0.0817390542709,0.0818615556636,0.0817390542709,0.0818921810117,0.0820453077526,0.0820453077526,0.0819228063599,0.0817084289227,0.0818309303154,0.0819840570562,0.0816165528782,0.0814940514855,0.0819534317081,0.0818615556636,0.0819534317081,0.0819534317081,0.0821678091453,0.0826884400642,0.0824434372788,0.0821984344935,0.0822596851898,0.0825659386715,0.0822290598416,0.0821371837971,0.0816778035745,0.0819228063599,0.0813715500928,0.0810346712629,0.0808202938257,0.0809427952184,0.0803915389513,0.080330288255,0.0803915389513,0.0803915389513,0.0802690375586,0.0799321587287,0.0801771615141,0.0798709080324,0.0800546601214,0.0799015333806,0.0805446656922,0.0802077868623,0.0799015333806,0.079442153158,0.0795340292025,0.0795340292025,0.0794727785062,0.0795034038543,0.0796565305952,0.0793502771135,0.0792277757208,0.0789827729354,0.0790133982836,0.0791971503726,0.0789521475872,0.0793809024616,0.0791971503726,0.0791971503726,0.0791358996763,0.0795034038543,0.0794115278098,0.0796871559434,0.0797790319879,0.0796871559434,0.0799015333806,0.0795034038543,0.0797484066397,0.0801159108178,0.0798402826842,0.0795646545507,0.0798709080324,0.079809657336,0.0802384122104,0.0808509191739,0.0810346712629,0.0809734205666,0.0810346712629,0.0806671670849,0.0806671670849,0.0810346712629,0.0809427952184,0.0811571726556,0.0808509191739,0.0809121698702,0.0808815445221,0.0808815445221,0.0807590431294,0.0811877980038,0.0814328007892,0.0809427952184,0.0810040459147,0.0808509191739,0.0805446656922,0.0802384122104,0.0800852854696,0.0800546601214,0.0797177812915,0.0795340292025,0.0790746489799,0.0795952798988,0.079442153158,0.079809657336,0.0801771615141,0.0798709080324,0.0796871559434,0.0797177812915,0.0799015333806,0.0797484066397,0.0800546601214,0.079809657336,0.0797484066397,0.0795646545507,0.0793196517653,0.079625905247,0.0794727785062,0.0797790319879,0.080330288255,0.0804221642995,0.0806059163885,0.0806671670849,0.0808509191739,0.0809734205666,0.0812796740483,0.081402175441,0.0815246768337,0.0814634261373,0.0811265473074,0.0814328007892,0.0814940514855,0.0815553021818,0.0813715500928,0.081218423352,0.0813102993965,0.0816778035745,0.0820453077526,0.0823209358861,0.0825965640197,0.0821984344935,0.0821371837971,0.082474062627,0.0827803161087,0.083178445635,0.0832703216795,0.0831478202868,0.083545949813,0.0832396963313,0.0830865695904,0.0833315723758,0.0836378258575,0.0836072005094,0.0837603272502,0.0840359553838,0.0840053300356,0.0838828286429,0.0836990765539,0.0832703216795,0.083362197724,0.083362197724,0.0831171949386,0.0833009470276,0.0830253188941,0.0822290598416,0.0819534317081,0.0821065584489,0.0820759331008,0.0828109414569,0.0828721921532,0.0832396963313,0.0833928230722,0.0829640681978,0.0833315723758,0.0836378258575,0.0835765751612,0.0834846991167,0.0832396963313,0.0830253188941,0.0832703216795,0.0829946935459,0.0831478202868,0.0835153244648,0.0836072005094,0.0834234484203,0.0838522032947,0.0839134539911,0.0841584567765,0.084250332821,0.0838215779466,0.0841890821246,0.0845565863027,0.0845565863027,0.0845872116509,0.0850465918734,0.0849547158289,0.0848934651326,0.0851078425698,0.0851997186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m <- 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ycorr <- 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altd  <- c(0, 36, 87, 131, 179, 193, 238, 290, 309, 445, 537, 558, 573, 597)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('36-JAG-GSE51537/JAG-GFP-replicate-1-GSM1247499/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) : 0,36,87,131,179,193,238,290,309,445,537,558,573,597',bty='n')
dev.off()