# R script for Peak Model
#  -- generated by MACS
p <- c(0.0428279873334,0.0499160400042,0.0571148504761,0.0642319324093,0.071344101698,0.0713159656437,0.0712735382602,0.0712878295894,0.0712083340708,0.0710792655041,0.071017634147,0.0711408968612,0.0709493037293,0.0708581965058,0.0708139827061,0.0708613227341,0.0709649348706,0.0708738276471,0.0709551095818,0.070957342602,0.0708693616067,0.0707367202077,0.070824701203,0.0708573032977,0.0708492644251,0.0708398857403,0.0706777684749,0.0708287206394,0.0707983515648,0.0709225074871,0.0710555954901,0.0710681004032,0.0710453235973,0.07110204231,0.0711118675988,0.0709734203473,0.0711377706329,0.0711154404311,0.0711328579885,0.0709877116765,0.071006022442,0.071065420779,0.0710229933954,0.071054255678,0.0710207603753,0.0711449162975,0.0709868184685,0.0709162550306,0.0707845068397,0.0707577105975,0.0706755354547,0.0706259624066,0.0707331473755,0.0706447197761,0.0707197492543,0.0705790689827,0.0706482926084,0.0705670106737,0.0706536518569,0.0707862932559,0.0706933996162,0.0706688363941,0.0706031856007,0.0705679038818,0.0705527193445,0.0706527586488,0.0706340012792,0.0707179628382,0.0706500790246,0.0705567387808,0.0705750495464,0.0705428940557,0.070521903666,0.0705509329284,0.0704968938399,0.0705093987529,0.0704428547514,0.0704129322809,0.0704727772219,0.0704897481753,0.0704665247654,0.070377650562,0.0703490679037,0.0704517868322,0.0704692043896,0.0703472814875,0.0703807767903,0.0703780971661,0.0703419222391,0.0703865826428,0.0705491465122,0.0706858073475,0.0707809340074,0.0707916525043,0.0708617693381,0.0709269735275,0.0709385852325,0.0709055365337,0.0709336725881,0.0709430512728,0.0708573032977,0.0707684290944,0.0707251085028,0.0706147973057,0.0706107778693,0.0706174769299,0.0705616514253,0.070739846436,0.070715729818,0.0707090307575,0.0707411862481,0.0708180021425,0.0708800801036,0.0709318861719,0.0709551095818,0.0710033428178,0.0710926636252,0.0709144686145,0.0709845854483,0.070993517529,0.0710596149265,0.0710881975848,0.0710484498256,0.07105336247,0.0709158084266,0.07093277938,0.0710229933954,0.0709564493939,0.0709680610989,0.0710448769933,0.071077479088,0.0710756926718,0.0711096345786,0.0711158870351,0.0712378099372,0.0712721984481,0.071259693535,0.0714325292973,0.0715383744541,0.0714986266948,0.0714387817539,0.0714249370287,0.0714535196871,0.0714566459153,0.0714669178082,0.0714508400629,0.0715388210581,0.0715035393392,0.0714097524915,0.0714070728672,0.0714937140504,0.0716290350736,0.0716326079059,0.0717018315316,0.071814822353,0.0718161621651,0.0718429584073,0.0719068227846,0.0719644347054,0.0720738526944,0.072141289904,0.0720716196743,0.0720859110034,0.072177464831,0.072104221769,0.072177464831,0.0721229791385,0.0722574069536,0.0723748638154,0.0723592326741,0.0722757177191,0.072309659626,0.0724043396818,0.0724356019644,0.0725557384503,0.0726705156878,0.072780826885,0.0728697010883,0.0729755462451,0.072975099641,0.0730327115618,0.0731537412558,0.0731376635105,0.0731233721813,0.0732336833785,0.0732506543319,0.0732100133645,0.0731912559949,0.0731492752155,0.0732051007201,0.0733815093147,0.0735440731841,0.0736606368378,0.0737897054045,0.0737785403036,0.0738857252724,0.073977725704,0.07404918235,0.0741679790238,0.0743649314041,0.0744319220096,0.0745132039444,0.0747400787952,0.0748423511196,0.0749084485171,0.0750504686008,0.0752179451147,0.0753086057342,0.0753032464858,0.0753939071053,0.0754667035633,0.0754729560198,0.0754229363677,0.0755323543567,0.0756703550042,0.0756658889638,0.0756998308706,0.0756417723458,0.0757708409125,0.0757681612883,0.0759075017478,0.0760120070924,0.0760696190132,0.0761084735644,0.0762437945876,0.0763349018112,0.0764921064322,0.0767667679149,0.0768453702254,0.0770199924039,0.0769994486182,0.0769628270872,0.0771164588759,0.0771897019379,0.0773366346661,0.077528674402,0.077637645787,0.0777233937621,0.0779248121828,0.0780185990306,0.0782244834916,0.0784303679526,0.0786058833392,0.0786777865891,0.0786442912864,0.078688505086,0.0787322722816,0.0788501757474,0.0788564282039,0.0789720986495,0.0791297498745,0.0793655568061,0.0795352663401,0.0798161802794,0.0799952684982,0.0801797159655,0.0803869402386,0.0804753678379,0.0807652138579,0.0808728454308,0.080984049836,0.0811207106714,0.0812283422443,0.0814632559677,0.0816655675965,0.0818071410762,0.0819531805963,0.0821166376738,0.0821572786412,0.0824422120168,0.0826204070275,0.0827919029777,0.0828910490739,0.0828298643208,0.0830786227694,0.0833121966808,0.083520760766,0.083702082005,0.0839946076493,0.084112511115,0.0842170164597,0.0842942789581,0.0844421048943,0.0846323582141,0.0846019891395,0.0846524553957,0.0847846501907,0.0850235833504,0.0850633311097,0.085114690574,0.0853429052369,0.0856184599277,0.0859114321759,0.0862825601307,0.0865773187951,0.0867251447313,0.0868716308554,0.0869453205215,0.0872976911067,0.087651401504,0.0879613447056,0.0883329192644,0.0887076200514,0.0889121647004,0.0894038757451,0.0900813740691,0.090756192769,0.091347943118,0.0918168773568,0.0922755397028,0.092664978423,0.0929615235036,0.0933022823838,0.0935577398929,0.0938230226909,0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m <- 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ycorr <- 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altd  <- c(262)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('A549-100nM-Dex-7h-H3K27ac.pooled.sorted.pseudoRep2.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) : 262',bty='n')
dev.off()