# R script for Peak Model
#  -- generated by MACS
p <- c(0.0426588238179,0.0497030382568,0.0567765909434,0.0638835285325,0.0708356815734,0.0707800400692,0.0707102352729,0.0706515587775,0.0705635440344,0.0704269694331,0.0703086047786,0.0703065814511,0.0704421443888,0.0704107828136,0.0704886809196,0.0704097711499,0.0705170075036,0.0704188761234,0.0703632346191,0.0704431560525,0.0704077478225,0.0704745176276,0.0701710185135,0.0701791118232,0.0701386452746,0.0703045581237,0.0702357649912,0.0704289927605,0.0705028442116,0.0704532726896,0.070604010583,0.070511949185,0.0707618301223,0.0706667337332,0.0706758387067,0.0704937392382,0.0705524157336,0.0704735059639,0.070526112477,0.070547357415,0.0704198877871,0.0704593426719,0.0703055697874,0.0702984881414,0.0704502376985,0.0706293021758,0.0705170075036,0.0703450246723,0.0703136630971,0.070296464814,0.0704987975567,0.0703409780174,0.0703146747608,0.0704815992736,0.0702377883186,0.0701143653455,0.0701801234869,0.0702317183363,0.0702135083895,0.0702337416637,0.0701143653455,0.0701760768321,0.0702590332566,0.0702135083895,0.0703753745837,0.0703622229554,0.070296464814,0.070073898797,0.0699808257353,0.0700233156113,0.0700192689564,0.0700273622661,0.0698796593639,0.0698442511339,0.0697410614351,0.0698179478774,0.0697835513111,0.0700253389387,0.0701194236641,0.0701649485312,0.070088062089,0.0702337416637,0.0703480596634,0.0703015231326,0.0704016778402,0.070239811646,0.0705291474682,0.0705433107601,0.0705777073264,0.0704037011677,0.0704340510791,0.0702731965486,0.0702802781946,0.0702640915752,0.0702165433806,0.0702711732211,0.0699474408327,0.0699545224787,0.0698209828685,0.0698705543905,0.0697329681254,0.0698584144259,0.0698037845854,0.0697673646917,0.0697339797891,0.0698189595411,0.0698371694879,0.0697916446208,0.0698634727445,0.0699737440893,0.0701831584781,0.0701679835223,0.0701831584781,0.0702519516106,0.0702671265663,0.0701659601949,0.070476540955,0.0703784095748,0.070476540955,0.0705038558753,0.0703086047786,0.0702145200532,0.0701052603721,0.0701609018763,0.0702084500709,0.0703045581237,0.0701295403012,0.070324791398,0.07033895469,0.070331873044,0.070504867539,0.0705858006361,0.0707800400692,0.0706940486535,0.0707881333789,0.0709135796794,0.0709752911659,0.0708700781397,0.0708012850072,0.070769923432,0.0708468098743,0.0708842414317,0.0708882880865,0.0710521776082,0.0709661861925,0.0709277429714,0.070784086724,0.0708640081574,0.0709368479448,0.0709732678385,0.0709550578916,0.0710299210065,0.0711958338555,0.0711462623335,0.0711988688467,0.0712909302446,0.0716237676064,0.071600499341,0.0715762194119,0.0714962979785,0.071565091111,0.0716804207744,0.0715094496068,0.071727968969,0.0718240770218,0.071844310296,0.0715853243853,0.0715681261022,0.0716632224913,0.0718281236766,0.071900963464,0.0718959051454,0.0721639960296,0.0720911562422,0.072123529481,0.0721822059764,0.0724786234446,0.0728802539389,0.0730755050357,0.0731544148054,0.0731898230353,0.073226242929,0.073212079637,0.0731139482568,0.0731938696902,0.0732282662565,0.0733031293713,0.0731139482568,0.0730704467171,0.0730077235669,0.0729126271778,0.0729905252837,0.0730785400268,0.0733365142738,0.0734245290169,0.0734811821849,0.0734993921317,0.0735509869811,0.0735024271229,0.0737543313876,0.0741043670326,0.0741377519351,0.0741478685723,0.0740770521123,0.0742368949791,0.0742277900056,0.0743673995981,0.0745697323409,0.0747690300925,0.0747558784642,0.0747831933845,0.0749976660918,0.07515245064,0.0753841216305,0.0752171971177,0.0753760283208,0.0754185181967,0.0753770399845,0.0755611627804,0.0756582824969,0.0755975826741,0.0755874660369,0.0754943929753,0.0755793727272,0.0757412389214,0.0757938454345,0.0759091750979,0.0761519743892,0.0762278491677,0.0765444999101,0.0769704103336,0.0772162446161,0.0774347639782,0.0775834785442,0.0777433214109,0.0779840973748,0.0782440949493,0.0783493079755,0.0783644829312,0.0783351446835,0.0781965467547,0.0782127333741,0.078453509338,0.0784949875503,0.0786153755322,0.0786801220099,0.0787054136027,0.078810626629,0.0789927260974,0.079089845814,0.0793245517955,0.079492487972,0.0796280509097,0.0799001884487,0.0800822879171,0.0800954395454,0.0801187078108,0.0802522474211,0.0804687434558,0.0805871081103,0.0807459393134,0.080952318711,0.0810423567815,0.0810423567815,0.0812305262323,0.0815684219127,0.081733323098,0.0818962009559,0.0818365127968,0.082055032159,0.0820530088315,0.0822179100169,0.0825042108479,0.0825719923167,0.0825669339981,0.0827004736083,0.0827156485641,0.082800628316,0.0830778241736,0.08328116858,0.083581632703,0.0836049009684,0.0835330728448,0.0838011637289,0.0840915112148,0.0843272288601,0.0848684689469,0.085242784521,0.0855189687149,0.0857465930505,0.0858113395281,0.0860774070849,0.0862706348542,0.0865225391189,0.0866500087468,0.0867198135431,0.0867592684279,0.0868290732242,0.0869899277547,0.0873005085148,0.0877709321417,0.0882110058572,0.0888857855542,0.089547413623,0.0903870945055,0.0911316789988,0.0919855231732,0.0927230260205,0.0934858204607,0.0941697051312,0.094788843324,0.0953371650569,0.0957489121884,0.0961029944882,0.0962709306647,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m <- 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ycorr <- 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altd  <- c(271)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('A549-100nM-Dex-8h-H3K27ac.pooled.sorted.pseudoRep1.MACS-2.1.0.p1e-1_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) : 271',bty='n')
dev.off()