# R script for Peak Model
#  -- generated by MACS
p <- c(0.0411917591242,0.0480954554146,0.0549229363159,0.0618159979009,0.0688437657549,0.0688189514421,0.0688065442858,0.0689323883003,0.0690777292749,0.0690670945694,0.0691025435876,0.0691397650567,0.0692549743658,0.0694003153403,0.0692673815221,0.0692124355439,0.0692638366203,0.0692266151512,0.068996196533,0.0690068312385,0.069132675253,0.0690635496676,0.0687728677185,0.068647023704,0.0686452512531,0.0685318143949,0.0686168920385,0.0686292991949,0.0686807002712,0.0687462809549,0.068530041944,0.0684573714567,0.0686718380167,0.0687090594858,0.0684857306713,0.068861490264,0.0686877900749,0.0685601736094,0.0684945929258,0.0686541135076,0.0687994544821,0.0688349035003,0.0687569156603,0.0688579453621,0.0690121485912,0.0687923646785,0.0688366759512,0.0689625199658,0.0690068312385,0.0688916219294,0.0687356462494,0.068822496344,0.0689164362421,0.0685708083149,0.0686027124313,0.0685584011585,0.0684609163585,0.0683616591076,0.0683563417549,0.0683971081258,0.0685229521404,0.068452054104,0.0682358150931,0.0686346165476,0.0685796705694,0.0688012269331,0.0690334180021,0.0689022566349,0.0688650351658,0.0686168920385,0.0684981378276,0.0686328440967,0.0687001972312,0.0684414193985,0.0686062573331,0.0682836712676,0.0680443903949,0.0681666895077,0.068296078424,0.0684431918494,0.0688384484021,0.0686558859585,0.0687321013476,0.0686771553694,0.0682021385258,0.0681578272531,0.0683102580313,0.0683138029331,0.0681968211731,0.0681613721549,0.067964630104,0.0680213485331,0.0678884147149,0.0677288941331,0.0680160311804,0.0680975639222,0.0679788097113,0.0679380433404,0.0678689177549,0.0678033370713,0.0678458758931,0.0679770372604,0.0682606294058,0.0685016827294,0.0685335868458,0.0686753829185,0.0686718380167,0.0685849879222,0.0685335868458,0.0685530838058,0.0684290122422,0.068159599704,0.0679486780458,0.0679025943222,0.0680869292167,0.068003624024,0.068120605784,0.0682730365622,0.0684431918494,0.0685264970422,0.0684414193985,0.0685034551804,0.0686789278203,0.0687196941912,0.0685070000822,0.0684538265549,0.0686062573331,0.068627526744,0.068530041944,0.0685087725331,0.0686399339003,0.0685619460603,0.0686062573331,0.0686151195876,0.0687551432094,0.0688792147731,0.0686948798785,0.068627526744,0.0686877900749,0.0685920777258,0.0686895625258,0.0691149507439,0.069171669173,0.0690670945694,0.0691078609403,0.0692744713258,0.0693932255367,0.0694676684748,0.0696307339585,0.0698186137548,0.0698203862057,0.0697282187584,0.0694800756312,0.0695102072966,0.0694269021039,0.0692797886785,0.0692620641694,0.0692549743658,0.0693577765185,0.0695917400385,0.0694286745548,0.0694605786712,0.0698257035584,0.0699692720821,0.0699763618857,0.0701057508021,0.0700383976675,0.0700011761984,0.0700437150202,0.0699869965912,0.0701908284457,0.0701926008966,0.0700153558057,0.070068529333,0.0703255347148,0.0707154739147,0.0709193057693,0.0710557844893,0.0710079283147,0.0709653894929,0.0710823712529,0.0711639039947,0.0712844306565,0.0711834009547,0.0713074725183,0.0707916893038,0.0709494374347,0.0710646467438,0.071197580562,0.0711816285038,0.0712011254638,0.0713092449692,0.071431544082,0.0718994711219,0.071780716911,0.0719207405328,0.0719969559219,0.0719065609256,0.0719473272965,0.0719136507292,0.0719331476892,0.0721458417983,0.0720891233692,0.0721015305255,0.0722256020892,0.0722504164019,0.0722326918928,0.0724560207073,0.0725109666855,0.0728814089255,0.0730107978418,0.07281228334,0.0730356121546,0.0729771212746,0.0727786067728,0.0730994203873,0.0730746060746,0.07324121646,0.0733262941036,0.0733422461618,0.0734007370418,0.0736027964454,0.0736169760527,0.0736276107582,0.0739838733909,0.0739785560381,0.0743986269036,0.0744163514126,0.0746946262053,0.0746857639508,0.0748807335508,0.0751643256962,0.0751235593253,0.0751200144235,0.0751129246199,0.0750969725617,0.0748364222781,0.074896685609,0.0746538598344,0.0748470569835,0.0747850212017,0.0748807335508,0.0751572358926,0.0756145282271,0.0760735930125,0.0764777118198,0.0767666213179,0.0768658785688,0.0773745719797,0.077542954816,0.0778478163724,0.077620942656,0.0777591938269,0.0778850378415,0.0776085354997,0.0774826914851,0.0775837211869,0.0778903551942,0.0778921276451,0.0779027623506,0.0779382113687,0.0781402707724,0.0781704024378,0.0782873841978,0.0784646292887,0.0788900175069,0.0792338729832,0.0794501119941,0.0794678365032,0.0797957399213,0.0800881943213,0.0802654394122,0.0804728161686,0.0806482888085,0.0809673299722,0.081125078103,0.0810967188885,0.0809584677176,0.0807900848813,0.0807032347867,0.0805986601831,0.0808609829176,0.0807688154703,0.0804338222486,0.0805454866558,0.0806926000813,0.0807812226267,0.0811587546703,0.0814919754412,0.0817649328812,0.082119423063,0.0819386330703,0.0824544162848,0.0829595647938,0.0831793487065,0.0829382953829,0.0832059354702,0.083326462132,0.083618916532,0.0840921609246,0.084669979921,0.0856395105682,0.0864956043572,0.0873995543208,0.0883726298698,0.0898685784369,0.0909639530987,0.0918165019859,0.0930288584076,0.0937183418112,0.0942217178693,0.0947180041239,0.0948296685311,0.094948422742,0.09500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m <- 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ycorr <- 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altd  <- c(243)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('Macaca_mulatta-male-liver-H3K27Ac-ERR572211.50mers.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) : 243',bty='n')
dev.off()