# R script for Peak Model
#  -- generated by MACS
p <- c(0.0318974790431,0.0372354245157,0.0426167679189,0.0475496660385,0.0524825641581,0.0522077105971,0.0520341188745,0.0520775168051,0.0521353807127,0.052091982782,0.051831595198,0.0515422756602,0.0516001395677,0.0512529561224,0.0516869354291,0.0516290715215,0.0520630508282,0.0523379043892,0.0518171292211,0.0523813023198,0.0529454754185,0.0526850878345,0.0526995538114,0.0536687742631,0.0539146958702,0.0537555701244,0.0537121721937,0.0539725597778,0.0542763452925,0.0537411041475,0.0535964443786,0.0541461515004,0.0537989680551,0.0532926588639,0.0528586795572,0.0537989680551,0.053538580471,0.0534951825404,0.0533071248408,0.0537266381706,0.0536109103555,0.0538712979395,0.0542329473618,0.0546379947147,0.0551587698828,0.0546235287378,0.0554480894206,0.0551732358597,0.0557084770046,0.055520419305,0.0548983822987,0.0542908112693,0.0542763452925,0.0544933349458,0.0547247905761,0.0550285760907,0.0548115864374,0.0549851781601,0.0546090627609,0.0548115864374,0.0557374089584,0.0567644933176,0.0569814829709,0.0574733261852,0.0573286664163,0.0572997344625,0.0570393468785,0.0570827448092,0.057632451931,0.0579507034226,0.0581242951453,0.0573865303239,0.0570104149247,0.0565619696411,0.0565475036642,0.0559833305655,0.0561713882651,0.056316048034,0.0560701264269,0.0559833305655,0.0561135243575,0.0566921634331,0.0571406087167,0.0569670169941,0.0572129386012,0.0583702167524,0.0586450703133,0.0586161383595,0.0585438084751,0.0585293424982,0.0587752641053,0.0586306043364,0.0586161383595,0.0588620599667,0.0586740022671,0.0585004105444,0.0591513795045,0.0607571029393,0.0609017627082,0.0609740925927,0.0608728307544,0.0614370038532,0.0620156429288,0.0623628263741,0.0625364180968,0.0625942820044,0.0621603026977,0.0611187523616,0.0612489461536,0.061596129599,0.0620301089057,0.0615816636221,0.0613936059225,0.0613502079918,0.0619722449981,0.0616684594834,0.0615237997145,0.0610319565002,0.061726323391,0.0621313707439,0.0623483603972,0.0634188426871,0.0635490364791,0.0635779684329,0.0633899107333,0.0638672879707,0.064098743601,0.065154759914,0.0645037909539,0.0648509743993,0.064619518769,0.0641855394623,0.0647641785379,0.0648220424455,0.0652126238215,0.0658346608278,0.0662975720883,0.0662541741576,0.0663120380652,0.0659937865736,0.0666881534643,0.0676429079391,0.0676429079391,0.0682938768992,0.0681492171303,0.0674693162164,0.0675850440315,0.0675850440315,0.0686410603445,0.0691763014895,0.0689882437899,0.0683228088529,0.0683806727605,0.0680190233382,0.0675416461009,0.0686555263214,0.0687857201134,0.0689448458592,0.0686265943676,0.0682649449454,0.0683083428761,0.0688001860903,0.0691473695357,0.0697838725189,0.0710134805545,0.0708543548088,0.0714329938844,0.0713172660692,0.0717367793991,0.0721852246827,0.071751245376,0.0717801773297,0.071476391815,0.071476391815,0.071606585607,0.0719248370986,0.071476391815,0.0724890101974,0.073197843065,0.0730531832961,0.0738922099557,0.0737620161637,0.0741381315629,0.0741381315629,0.0741525975397,0.0745865768465,0.0751362839683,0.0749482262687,0.074514246962,0.0748180324767,0.075570263275,0.0761055044199,0.0758740487897,0.0766118136111,0.0763224940733,0.0760765724662,0.0768288032645,0.0773061805018,0.0776533639472,0.0777112278548,0.0780150133695,0.0776533639472,0.0784923906068,0.0783621968148,0.078868506006,0.0790276317518,0.0780294793463,0.0776244319934,0.077812489693,0.0783621968148,0.0785357885375,0.0797075326656,0.0796930666887,0.080445297487,0.0813277220773,0.0811830623084,0.0827019898819,0.0835988804491,0.0836567443567,0.084003927802,0.0835554825184,0.0835988804491,0.0840907236634,0.0846982946928,0.0842353834323,0.0856819811213,0.0849876142306,0.084799556531,0.0853781956066,0.0856675151444,0.0853926615835,0.0856819811213,0.0864631438734,0.0858266408902,0.0865065418041,0.0858411068671,0.0858845047978,0.0862750861738,0.0859423687053,0.0854215935373,0.0865354737578,0.0868826572032,0.0866367355961,0.0871430447872,0.0874034323713,0.0876927519091,0.0887053702914,0.0891104176443,0.0895588629279,0.0897903185582,0.0898771144195,0.0898915803964,0.0904991514258,0.0908174029174,0.0915551677388,0.092191670722,0.0924809902598,0.0922929325602,0.0934212787576,0.0944483631169,0.0945351589782,0.0946219548395,0.0951427300076,0.0954465155223,0.094824478516,0.0948678764467,0.0946219548395,0.0950414681694,0.095215059892,0.0948823424236,0.0957358350601,0.0967773853962,0.0968931132113,0.0972692286105,0.0980793233163,0.0992366014675,0.100119026058,0.101203974325,0.10201406903,0.10262164006,0.102491446268,0.102549310175,0.102737367875,0.102983289482,0.103489598673,0.103619792465,0.104053771772,0.104690274755,0.104227363495,0.10587648486,0.106845705312,0.10759793611,0.10759793611,0.107872789671,0.108176575186,0.108523758631,0.108176575186,0.107974051509,0.109102397707,0.109478513106,0.11015841402,0.110375403673,0.112010059062,0.113572384566,0.11559762133,0.116653637643,0.119243047507,0.121760127486,0.122989735521,0.12420487758,0.125723805154,0.12783583778,0.12848680674,0.130106996151,0.13062777132,0.131264274303,0.131596991771,0.130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m <- 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ycorr <- 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altd  <- c(332)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('Macaca_mulatta-male-liver-H3K4me3-ERR572239.50mers.unique.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) : 332',bty='n')
dev.off()