# R script for Peak Model
#  -- generated by MACS
p <- c(0.0217112424746,0.0255436183527,0.0290260816506,0.0325918574676,0.0362409458037,0.0364075708419,0.0367074959106,0.0365242083686,0.0367741459259,0.0366575083992,0.0364575583533,0.0361076457732,0.0360243332541,0.0363742458342,0.0361409707808,0.0361909582923,0.0360576582617,0.0362409458037,0.0358243832083,0.0359576832388,0.0356077706586,0.0355411206434,0.0356910831777,0.0355577831472,0.0356577581701,0.0358577082159,0.035574445651,0.0354578081243,0.0352745205823,0.0355077956357,0.0358243832083,0.0364742208572,0.0368074709335,0.0371907085213,0.0369241084602,0.0368241334373,0.037124058506,0.0373906585671,0.0378738711779,0.0379905087046,0.0378905336817,0.037857208674,0.0379238586893,0.0368241334373,0.037224033529,0.037307346048,0.0373906585671,0.0373739960633,0.037224033529,0.0372906835442,0.0375572836053,0.0371907085213,0.0370907334984,0.0377905586588,0.0377905586588,0.0378072211626,0.0378072211626,0.0377738961549,0.0380238337122,0.0376239336206,0.0372740210404,0.0375406211015,0.0370740709946,0.0372073710251,0.0374573085824,0.0373906585671,0.0373573335595,0.0372406960328,0.0377738961549,0.0382904337733,0.0385570338344,0.0384570588115,0.0392901840024,0.0394401465367,0.0396067715749,0.0395734465673,0.0399233591474,0.0406731718192,0.0402566092238,0.0408064718498,0.0415062970101,0.0419895096208,0.0419395221094,0.0422227846743,0.0421061471476,0.0421228096514,0.0420728221399,0.0417562345674,0.0415062970101,0.0407731468421,0.0399733466589,0.0396234340787,0.0395401215596,0.0391735464756,0.0391568839718,0.0393901590253,0.0395234590558,0.0397234091016,0.0402066217123,0.0410897344147,0.0412730219567,0.0418895345979,0.0422061221705,0.0425726972545,0.0425726972545,0.0429892598499,0.0427893098041,0.0426560097736,0.042339422201,0.0414896345063,0.0420061721247,0.0418562095903,0.0418062220789,0.0416395970407,0.0424060722163,0.0422061221705,0.0422394471781,0.0418895345979,0.0422561096819,0.0426893347812,0.0426060222621,0.0422894346896,0.0419561846132,0.0419561846132,0.0418728720941,0.0416729220483,0.0418728720941,0.0421394721552,0.0422894346896,0.0426560097736,0.0424060722163,0.0431558848881,0.0434224849492,0.0435391224759,0.0434891349644,0.0433391724301,0.0435391224759,0.0443222601553,0.0444722226897,0.0446055227202,0.0453719978959,0.0447554852546,0.0447054977431,0.0452053728577,0.0448054727661,0.046271773102,0.045905198018,0.0457052479722,0.045088735331,0.0449720978042,0.0444555601859,0.0450220853157,0.0455886104455,0.045538622934,0.0459385230257,0.0450220853157,0.0456052729493,0.0456719229646,0.0466216856822,0.0469216107509,0.0472548608273,0.0468049732242,0.0463717481249,0.0465383731631,0.0470715732853,0.0474048233616,0.0475381233922,0.047738073438,0.0479546859876,0.0481546360334,0.0489044487052,0.0495876113618,0.050204124003,0.0505207115756,0.0506873366137,0.0505040490717,0.0508206366443,0.0506873366137,0.0508039741405,0.0504207365527,0.049470973835,0.0492543612854,0.0495876113618,0.0497042488885,0.0497042488885,0.0503040990259,0.0513205117588,0.0520203369192,0.0517537368581,0.0525035495299,0.0531867121864,0.0538532123391,0.0545363749956,0.054136474904,0.0547196625376,0.0549696000949,0.0543364249498,0.0542531124307,0.0548029750567,0.0555194627209,0.0558527127973,0.0559860128278,0.0555861127362,0.0562026253774,0.0563859129194,0.0564858879423,0.056702500492,0.057152388095,0.0574023256523,0.0571024005836,0.0575522881867,0.0579688507821,0.0573856631485,0.0577689007363,0.057702250721,0.0580521633012,0.0577855632401,0.0583687508737,0.0585353759119,0.0587353259577,0.0589352760035,0.0590185885226,0.0597850636983,0.0603182638204,0.0605848638815,0.0611347265075,0.0619678516984,0.06145131408,0.061634601622,0.0617179141411,0.0616179391182,0.0622011267518,0.062917614416,0.0624843893167,0.0636174395763,0.0636174395763,0.0636341020802,0.064567202294,0.0649004523703,0.0652670274543,0.0658502150879,0.0660168401261,0.0657669025688,0.0665833652559,0.0658835400956,0.065933527607,0.0662501151796,0.0659501901108,0.0663334276986,0.0664500652254,0.0665333777445,0.0667000027826,0.0669999278514,0.0677830655308,0.0681163156072,0.0687828157599,0.0692826908744,0.069499303424,0.0697659034851,0.0701824660806,0.0710155912714,0.071332178844,0.0718320539585,0.0717154164318,0.0719653539891,0.072065329012,0.0721653040349,0.0732317042792,0.0741481419892,0.0749646046763,0.0751812172259,0.0754144922793,0.0762142924626,0.0770807426611,0.0777139178062,0.0781138178978,0.0794468182033,0.0806798434858,0.080563205959,0.0805132184476,0.0815962811957,0.082212793837,0.0827793189668,0.0828959564935,0.083129231547,0.0842789443104,0.084228956799,0.0835957816539,0.0837290816844,0.084312269318,0.0839123692264,0.0845622068753,0.0846455193944,0.085045419486,0.0859951822036,0.086511719822,0.0871448949671,0.0882112952114,0.0893943329825,0.0910272583566,0.0921936336239,0.0927101712422,0.0934266589064,0.0942264590896,0.0950262592729,0.0950429217767,0.0957094219294,0.0965925346318,0.097575622357,0.0976422723723,0.0983420975326,0.0992751977464,0.0995751228152,0.10007499793,0.100224960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m <- 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ycorr <- 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altd  <- c(233)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('A549-100nM-Dex-7h-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) : 233',bty='n')
dev.off()