# R script for Peak Model
#  -- generated by MACS
p <- c(0.0382073293546,0.0442287182211,0.0501962071872,0.0567180951282,0.0628164838523,0.0627779839235,0.0624391845499,0.0625161844076,0.0619617854327,0.0621927850055,0.0623544847066,0.0628703837527,0.0631629832116,0.0632861829838,0.0638405819588,0.063963781731,0.0638251819872,0.0638790818876,0.0641408814035,0.0639483817594,0.0642178812611,0.063994581674,0.0645643806205,0.0643487810191,0.0643872809479,0.0644642808055,0.0649416799228,0.0651418795527,0.0650725796808,0.0655114788693,0.0653728791255,0.0651880794672,0.0647568802645,0.0645412806632,0.0640099816455,0.0642640811757,0.0639175818164,0.0636095823859,0.0638790818876,0.0635864824286,0.0636172823716,0.0637635821011,0.0642255812469,0.0644334808625,0.0646567804496,0.0642178812611,0.0646952803784,0.0644719807913,0.0645258806916,0.0643102810903,0.0645643806205,0.0650725796808,0.0647645802503,0.064903179994,0.0652034794388,0.0648492800937,0.0646413804781,0.0647029803642,0.0648954800083,0.0653035792537,0.0650263797662,0.0645643806205,0.0647645802503,0.0651572795242,0.0647645802503,0.0653805791113,0.0651803794815,0.0658733782001,0.0651803794815,0.0647722802361,0.064287181133,0.06471068035,0.0640484815744,0.0638174820015,0.0640176816313,0.0643025811045,0.0641023814747,0.0635633824713,0.0637789820727,0.0639791817025,0.0645258806916,0.0644796807771,0.0651110796096,0.0652188794103,0.0655037788835,0.0652188794103,0.0657347784564,0.0658502782428,0.0657655783994,0.06607357783,0.0666048768476,0.0665432769615,0.0664816770754,0.0663892772462,0.0664431771466,0.0661274777303,0.065973478015,0.0665047770327,0.0667742765344,0.0663738772747,0.0661274777303,0.066266077474,0.0667280766198,0.0665047770327,0.0663661772889,0.0667742765344,0.0671669758083,0.0665432769615,0.0666741767194,0.0667819765201,0.0670668759933,0.0668974763066,0.0658810781859,0.0659272781005,0.0657886783567,0.0658887781716,0.0656269786557,0.0657501784279,0.0658502782428,0.0657886783567,0.0658271782855,0.0654498789832,0.0660966777872,0.0659041781432,0.065650078613,0.0652804792964,0.0657116784991,0.0656115786842,0.0656885785418,0.065973478015,0.0656808785561,0.0661351777161,0.0661582776733,0.0665124770184,0.0669128762781,0.0676982748259,0.0670822759649,0.067467275253,0.0676135749825,0.0680216742279,0.0684374734591,0.0686222731174,0.0684913733595,0.0689841724483,0.06879937279,0.0681217740428,0.0687608728611,0.069284471893,0.0690765722774,0.0684528734306,0.068214173872,0.0679369743845,0.0682988737154,0.068052474171,0.0681217740428,0.0683142736869,0.0681756739432,0.068083274114,0.068214173872,0.0687454728896,0.0691304721778,0.0698850707825,0.0695000714944,0.0694307716225,0.0698003709391,0.0701776702415,0.0707089692591,0.0704933696578,0.0705318695866,0.0705241696008,0.0707012692734,0.0705857694869,0.0711478684476,0.0713326681059,0.0717484673371,0.0720333668103,0.0718870670808,0.0719332669954,0.0719717669242,0.0724183660984,0.0718793670951,0.0716252675649,0.0717330673656,0.0715944676218,0.071555967693,0.0716329675506,0.0716637674937,0.0718100672232,0.0721873665256,0.0717561673228,0.0722720663689,0.0728418653154,0.0729419651303,0.0731421647601,0.0729496651161,0.0728341653296,0.0733038644612,0.0736426638347,0.0738890633791,0.0739429632795,0.0738197635073,0.0735733639629,0.0737273636781,0.0737273636781,0.074089263009,0.0743356625534,0.0738890633791,0.0738890633791,0.0735579639913,0.0739198633222,0.0741662628666,0.0747129618557,0.0743356625534,0.0741431629093,0.073958363251,0.0745589621405,0.0744819622829,0.0747745617418,0.0749824613574,0.07561386019,0.0757986598483,0.075452160489,0.0760835593215,0.0767611580686,0.0772231572144,0.0769536577127,0.077269357129,0.0773386570008,0.0774079568727,0.0770460575418,0.0772077572429,0.077461856773,0.0774695567588,0.0773925569012,0.0772847571005,0.0772154572286,0.0776928563459,0.07788535599,0.0785706547229,0.0787554543812,0.0790172538971,0.0794484530998,0.0799720521317,0.0803570514198,0.0807266507364,0.0809576503093,0.08106545011,0.081358049569,0.0812502497683,0.0810346501669,0.0814042494835,0.0814350494266,0.0814966493127,0.0823051478178,0.0829827465649,0.08333694591,0.0837065452266,0.0840684445574,0.0843379440591,0.0853543421798,0.0849000430198,0.0855930417385,0.0858779412117,0.0858240413113,0.0857932413683,0.0854390420232,0.0851002426497,0.0849308429629,0.0852157424361,0.0852311424076,0.0859934409981,0.0860242409412,0.0863707403005,0.0866864397168,0.086355340329,0.0871099389337,0.0874025383927,0.0877798376951,0.0877798376951,0.0879184374388,0.0883265366842,0.0885113363425,0.0883034367269,0.0883188366985,0.0886730360436,0.0891581351466,0.0897125341215,0.0897664340219,0.0900975334097,0.0901745332673,0.0899820336232,0.0902977330395,0.090898331929,0.0908059320998,0.0915066308042,0.0916683305053,0.0913295311317,0.0920456298076,0.0928079283981,0.0936164269032,0.0940399261202,0.0941477259209,0.0945481251805,0.095441323529,0.0955106234009,0.0966194213507,0.0983442181615,0.0996301157839,0.0999073152714,0.10054641409,0.101431912452,0.102509910459,0.102833309861,0.103949807797,0.105151005576,0.1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m <- 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ycorr <- 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altd  <- c(298)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('Cavia_porcellus-male-liver-H3K4me3-ERR572170.50mers.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) : 298',bty='n')
dev.off()