# R script for Peak Model
#  -- generated by MACS
p <- c(0.0444803595753,0.051662220815,0.0595517837096,0.0668384896389,0.0744135184646,0.0744921519818,0.0744659408094,0.0749377419127,0.0746756301887,0.0749639530851,0.0750950089472,0.0752260648092,0.0747280525335,0.0745969966714,0.074439729637,0.0748328972231,0.075147431292,0.0747018413611,0.0748591083955,0.0748853195679,0.0747018413611,0.0747280525335,0.0747018413611,0.0749377419127,0.0749115307403,0.0746756301887,0.0751736424644,0.0753046983264,0.0755405988781,0.0755405988781,0.0756454435677,0.0756978659126,0.075986188809,0.0763793563951,0.0767725239813,0.0771132692226,0.0766414681192,0.0767201016364,0.0769822133605,0.0766676792916,0.0765366234296,0.0769822133605,0.0769560021881,0.076562834602,0.0763269340503,0.0765104122572,0.0769560021881,0.0771656915674,0.0769035798433,0.0772443250846,0.0777685485327,0.0778733932224,0.0780306602568,0.0780044490844,0.0782141384637,0.0777161261879,0.0774278032914,0.0774802256363,0.0774540144638,0.077139480395,0.0768511574985,0.0767201016364,0.076693890464,0.0768511574985,0.0767987351537,0.0772443250846,0.0772181139122,0.0769297910157,0.0773229586018,0.0777947597051,0.0777685485327,0.0775588591535,0.0775588591535,0.077401592119,0.0773491697742,0.0770608468777,0.077270536257,0.0776112814983,0.077270536257,0.0767987351537,0.0769560021881,0.0773229586018,0.0771919027398,0.0775850703259,0.0775588591535,0.0778996043948,0.0778209708776,0.0779258155672,0.0782927719809,0.0782141384637,0.0782403496361,0.0782141384637,0.0785810948774,0.0790528959807,0.0789742624635,0.0786073060498,0.0783714054981,0.0782927719809,0.07784718205,0.0780306602568,0.0780830826016,0.07784718205,0.0777161261879,0.0774540144638,0.0776899150155,0.0776374926707,0.0782927719809,0.0780044490844,0.0778733932224,0.0782927719809,0.0779520267396,0.0783451943257,0.0778996043948,0.0777685485327,0.0773753809466,0.0773491697742,0.0771132692226,0.0774540144638,0.0774278032914,0.0770608468777,0.0774540144638,0.0772967474294,0.0774802256363,0.0771656915674,0.0774278032914,0.0772181139122,0.076562834602,0.076562834602,0.0766414681192,0.0767463128088,0.0766414681192,0.0760648223263,0.0761958781883,0.0766152569468,0.0768511574985,0.0773229586018,0.0772181139122,0.0768511574985,0.0772181139122,0.0773753809466,0.0773491697742,0.0777947597051,0.0779520267396,0.07784718205,0.0777423373603,0.077978237912,0.0783451943257,0.0783714054981,0.0781879272913,0.0782141384637,0.0776374926707,0.0777947597051,0.0778996043948,0.077978237912,0.0784238278429,0.0780830826016,0.0787121507394,0.0790266848083,0.0791839518427,0.078816995429,0.0794722747392,0.0792363741876,0.0792101630151,0.0791839518427,0.0787383619118,0.0790004736359,0.0786335172222,0.0790004736359,0.0791315294979,0.0792887965324,0.079524697084,0.0799178646701,0.0800751317046,0.079970287015,0.0800489205322,0.0797081752909,0.0796819641185,0.07926258536,0.0792887965324,0.0796295417737,0.0796295417737,0.0794198523944,0.0792363741876,0.079393641222,0.0794984859116,0.0798654423253,0.0796033306013,0.0795771194288,0.07926258536,0.0789218401187,0.0786335172222,0.077978237912,0.0780044490844,0.0778996043948,0.0777423373603,0.0771919027398,0.0773229586018,0.077139480395,0.0773229586018,0.0770608468777,0.0769822133605,0.0773753809466,0.0771919027398,0.0769297910157,0.07643177874,0.0763531452227,0.0761696670159,0.0761434558435,0.0759337664642,0.0761696670159,0.0763007228779,0.0763793563951,0.0762483005331,0.0763793563951,0.0766676792916,0.0768773686709,0.0767725239813,0.0769035798433,0.0770608468777,0.0767463128088,0.0765890457744,0.07643177874,0.0766152569468,0.0765104122572,0.076562834602,0.0768511574985,0.0774278032914,0.0775064368087,0.0772181139122,0.0776374926707,0.0775064368087,0.0775064368087,0.0772181139122,0.0774540144638,0.0775326479811,0.0777161261879,0.0771656915674,0.0769560021881,0.0775850703259,0.077401592119,0.0778209708776,0.0781355049464,0.0780830826016,0.0781355049464,0.0779258155672,0.0776899150155,0.0783976166705,0.0788694177738,0.0789742624635,0.0789480512911,0.0786073060498,0.0787907842566,0.0791315294979,0.0791577406703,0.079524697084,0.0796819641185,0.0791839518427,0.0790266848083,0.0788956289463,0.0791577406703,0.0795509082564,0.079393641222,0.0797081752909,0.079970287015,0.0797868088081,0.0796295417737,0.0795509082564,0.0797081752909,0.0792101630151,0.0793412188772,0.0793150077048,0.0794198523944,0.0790004736359,0.0787121507394,0.0787383619118,0.0787645730842,0.078685939567,0.078685939567,0.0790004736359,0.0785286725326,0.0784500390153,0.0781617161188,0.0782403496361,0.0780044490844,0.0781879272913,0.077978237912,0.0781617161188,0.0780044490844,0.0781355049464,0.0783189831533,0.0780306602568,0.0783714054981,0.0786335172222,0.0791577406703,0.07926258536,0.0798916534977,0.0804420881183,0.0805731439803,0.0807566221872,0.0810449450837,0.081647802049,0.0818837026007,0.0820671808076,0.0817002243938,0.0819885472903,0.0819361249455,0.0819885472903,0.0820671808076,0.0819623361179,0.0820147584627,0.0818312802559,0.0812808456353,0.0815953797042,0.0819885472903,0.0820671808076,0.0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m <- 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ycorr <- 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altd  <- c(2, 95, 540)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('06-PIF3-GSE39215/P3M-ChIP-4-GSM958272/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) : 2,95,540',bty='n')
dev.off()