# R script for Peak Model
#  -- generated by MACS
p <- c(0.0189656129884,0.0222876942178,0.0253866505885,0.0289814399784,0.0323531045097,0.0320308130472,0.0324522711136,0.0329976874348,0.0325514377174,0.032824145878,0.0331216456896,0.0333943538502,0.0333695621993,0.0323531045097,0.0323778961607,0.0325514377174,0.0317828965375,0.0312126885653,0.0318076881885,0.0322043546039,0.0324274794626,0.0322539379058,0.0324274794626,0.0332208122935,0.0331216456896,0.0325762293684,0.0326258126703,0.0329481041329,0.03287372918,0.0326753959722,0.0323778961607,0.0327745625761,0.032848937529,0.0325762293684,0.0329233124819,0.0330224790858,0.0333199788973,0.0334935204541,0.033592687058,0.0338901868695,0.0345843530966,0.0339149785205,0.0340141451244,0.0345347697946,0.034311644936,0.0346835197004,0.0345099781437,0.0338406035676,0.0337662286147,0.0338158119167,0.0334687288031,0.0342124783321,0.0339893534734,0.0341628950302,0.034286853285,0.0342124783321,0.0339645618224,0.0347826863043,0.0349562278611,0.0346587280495,0.0345595614456,0.0339645618224,0.0344108115398,0.0340637284263,0.0334935204541,0.0337662286147,0.0332703955954,0.0323283128587,0.0331464373406,0.0331464373406,0.0333447705483,0.0333695621993,0.0330968540387,0.0334191455012,0.0342372699831,0.0344603948417,0.0356256024371,0.0357991439939,0.0353281026255,0.0356008107862,0.0360966438055,0.0366668517777,0.0365181018719,0.036394143617,0.0360966438055,0.0361958104093,0.0356503940881,0.0356008107862,0.0353281026255,0.0354272692294,0.034981019512,0.0346091447475,0.0349314362101,0.0350553944649,0.0352537276726,0.0353033109746,0.0359974772016,0.0367660183815,0.0373858096557,0.0377328927692,0.0377576844201,0.0375841428634,0.0374353929576,0.0376833094672,0.0377576844201,0.037832059373,0.037113101495,0.037113101495,0.0367660183815,0.0366668517777,0.037137893146,0.0373858096557,0.037881642675,0.0379064343259,0.0379312259769,0.0380056009298,0.0381047675336,0.0381047675336,0.0383031007414,0.0382039341375,0.037832059373,0.0377576844201,0.0374601846085,0.0373858096557,0.0375345595614,0.0374353929576,0.0379808092788,0.0380799758827,0.0383031007414,0.0388485170626,0.0395674749406,0.0400633079599,0.0405095576773,0.0405095576773,0.0408814324418,0.0410301823476,0.0409062240927,0.0412780988572,0.0409062240927,0.0406087242811,0.0396418498935,0.0399393497051,0.039964141356,0.0401624745638,0.0397162248464,0.0397410164974,0.0395922665916,0.0391460168742,0.0398897664031,0.039988933007,0.0404351827244,0.0407574741869,0.0406583075831,0.0402368495167,0.0408070574889,0.0410301823476,0.0411045573004,0.0415508070178,0.0411789322533,0.0410301823476,0.041426848763,0.0410053906966,0.0411789322533,0.0419474734333,0.0412533072062,0.040707890885,0.0420714316881,0.0419722650842,0.0422697648958,0.042864764519,0.0427903895661,0.0427160146132,0.0428895561699,0.0425672647074,0.0430878893777,0.0441539303692,0.0434597641421,0.044253096973,0.0440795554163,0.0437820556047,0.0440547637653,0.0445753884356,0.0448728882472,0.0454430962194,0.0452695546626,0.0453687212665,0.0453439296155,0.0447241383414,0.0447985132943,0.0458149709839,0.0462116373993,0.0465587205128,0.0461868457483,0.0458149709839,0.0469553869283,0.0463108040032,0.0467570537205,0.0469058036263,0.0468810119754,0.0465339288618,0.0466826787676,0.0464595539089,0.0466578871167,0.0472776783908,0.047104136834,0.0472528867398,0.0465587205128,0.0473272616927,0.0478974696649,0.0484676776371,0.0486908024958,0.0483437193823,0.0489387190055,0.0488643440526,0.0489139273545,0.0498808017422,0.0512691341962,0.0510708009885,0.0511699675924,0.0501783015537,0.0504262180634,0.0518145505175,0.0513683008001,0.051393092451,0.0516410089607,0.0520128837252,0.0515170507059,0.0513187174981,0.0521864252819,0.052855799858,0.0532028829715,0.0527318416032,0.0537978825947,0.054293715614,0.054293715614,0.0538970491985,0.0538970491985,0.0550374651429,0.0551862150487,0.0550622567939,0.0555332981622,0.0555085065113,0.0554589232093,0.0552357983507,0.0554589232093,0.0558555896248,0.0563018393422,0.0565497558518,0.0566489224557,0.0575166302395,0.0575414218904,0.0586570461839,0.0594007957128,0.0602437118456,0.0602189201947,0.059971003685,0.0602437118456,0.0609130864217,0.0611114196294,0.0613097528372,0.0612849611862,0.0608139198179,0.0613097528372,0.0618551691584,0.0624997520835,0.0642103760001,0.0655491251522,0.0655243335013,0.0658466249638,0.0659209999167,0.0663424579831,0.0676068321823,0.0669126659553,0.0672101657669,0.0680778735507,0.0680034985978,0.0682762067584,0.0676564154843,0.0679787069468,0.0689703729854,0.0693670394009,0.0693174560989,0.0697389141654,0.0701107889298,0.0694166227028,0.0697389141654,0.0695653726086,0.0708545384588,0.0715487046858,0.0718957877993,0.0724412041206,0.0724412041206,0.0734824534611,0.0736807866688,0.0753170356325,0.0753914105854,0.0758128686518,0.0764822432279,0.0762591183692,0.0774491176156,0.0778953673329,0.0787134918148,0.0798786994102,0.0810686986565,0.0818372398364,0.083597447055,0.0848618212542,0.0851345294148,0.0862997370102,0.0870930698411,0.0879855692758,0.0892003601731,0.0895226516357,0.0905391093252,0.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m <- 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ycorr <- 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altd  <- c(215)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('A549-100nM-Dex-8h-p300.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) : 215',bty='n')
dev.off()