# R script for Peak Model
#  -- generated by MACS
p <- c(0.0258949857854,0.0301579366342,0.0347463035782,0.0395055139724,0.0438010064306,0.0439799852831,0.0440776101117,0.0444274324141,0.0439555790759,0.0439962560878,0.0439067666616,0.0441020163188,0.044020662295,0.0436545691877,0.0441833703426,0.044785390119,0.0450131813857,0.0448097963261,0.0450782646048,0.0456721489787,0.0455419825406,0.0453874098953,0.0454036807001,0.045550117943,0.0448992857523,0.0447121714975,0.0448179317285,0.0448992857523,0.0445982758642,0.0441670995379,0.0442077765498,0.0445250572427,0.0447040360952,0.0446389528761,0.0448260671309,0.0445982758642,0.0445413280475,0.0447935255214,0.0452816496644,0.0454850347239,0.0456233365644,0.045720961393,0.0456965551859,0.0460545128907,0.0462904395599,0.0465426370337,0.0462904395599,0.0462416271456,0.0459162110502,0.0459650234645,0.0460057004764,0.0459080756479,0.0460870545003,0.045655878174,0.0456396073692,0.0455257117358,0.0462985749622,0.0462172209384,0.0468273761171,0.0471609276149,0.0473073648577,0.0473724480768,0.0474049896863,0.0478605722198,0.0480232802675,0.0483568317652,0.0482348007294,0.0486903832629,0.0484300503866,0.0483080193509,0.048267342339,0.0479012492317,0.0476490517578,0.047356177272,0.0472748232482,0.0471934692244,0.0472992294554,0.0472829586506,0.0476571871602,0.0479907386579,0.0484219149842,0.0487636018843,0.0490402055653,0.0495934129274,0.049796797987,0.0496991731584,0.0495608713179,0.0503418699466,0.0499106936203,0.0495283297083,0.0496747669512,0.0498862874132,0.0501303494847,0.049861881206,0.0497561209751,0.0500652662656,0.0501384848871,0.0496340899393,0.0499757768394,0.0503011929347,0.0504150885681,0.0504069531657,0.0499595060346,0.0503418699466,0.0509927021373,0.0512448996112,0.0514076076588,0.0513099828302,0.0512286288064,0.0512530350136,0.0515296386946,0.0518225131804,0.0529207925021,0.0524570745663,0.0519526796185,0.0518062423756,0.0518387839851,0.0520747106542,0.0523838559448,0.0526767304306,0.0523187727257,0.0522862311162,0.0522455541043,0.0527011366377,0.0532543439998,0.0534739998641,0.0538970407881,0.0539295823976,0.0538970407881,0.0540516134333,0.0540190718238,0.0544421127477,0.0540109364214,0.0547837996478,0.054702445624,0.0548244766597,0.0548895598788,0.0550359971217,0.0555485274718,0.055743777129,0.0565898589769,0.0566386713912,0.0571105247294,0.0571430663389,0.0575579718605,0.0575986488724,0.0577776277248,0.0580623668082,0.0580867730154,0.0577369507129,0.0574033992152,0.0573708576056,0.0572650973747,0.0572650973747,0.0574522116295,0.0578183047367,0.0576474612867,0.058078637613,0.0582982934773,0.0591443753252,0.0591443753252,0.0596813118824,0.0599091031492,0.0597382596991,0.0596243640658,0.05950233303,0.0598521553325,0.0597626659063,0.0597952075158,0.0594860622253,0.0599172385516,0.0602426546469,0.0607633203994,0.0613327985662,0.0615443190282,0.0617558394901,0.0620812555855,0.062113797195,0.0624148070832,0.0629029312262,0.0629598790428,0.0629029312262,0.0626425983499,0.062219557426,0.0623985362784,0.0623334530593,0.0625124319118,0.0626181921427,0.0629598790428,0.0632527535286,0.0632283473215,0.0633259721501,0.0639117211217,0.0645869595195,0.0650344066505,0.065766592865,0.0659374363151,0.0665231852866,0.0665475914938,0.0663360710318,0.0669380908082,0.0670682572463,0.0671496112701,0.0675889229988,0.0682072135799,0.0686302545039,0.0691102432445,0.069354305316,0.0694519301446,0.0702003871638,0.0706152926853,0.0713962913141,0.0714206975213,0.0716159471785,0.0717379782142,0.0720308527,0.0720227172976,0.0717054366047,0.0721447483334,0.0724864352335,0.0724782998311,0.0722098315524,0.0728037159264,0.0729176115598,0.0731047258146,0.0731698090336,0.0733487878861,0.0740891095029,0.0738206412243,0.0732023506432,0.0737880996147,0.0744714734149,0.074430796403,0.0747318062912,0.0751873888246,0.075301284458,0.0759927936606,0.076000929063,0.0770097189585,0.0780266442563,0.0779941026468,0.07759546793,0.0780998628778,0.078189352304,0.0783276541445,0.078954080128,0.0788971323113,0.0797676203663,0.0800930364617,0.0802394737045,0.0807031916404,0.0818990957907,0.0825011155671,0.0834854992554,0.0836482073031,0.0839329463865,0.0847627574296,0.0849173300748,0.0851044443296,0.0851288505368,0.0856495162893,0.0856332454845,0.0854379958274,0.0854624020345,0.0862840776752,0.086088828018,0.0860400156037,0.0867559310134,0.0873579507898,0.0881877618328,0.0883341990757,0.089253499545,0.0895382386284,0.0896684050666,0.0893104473617,0.090717871974,0.0911409128979,0.0920032655505,0.0922066506101,0.0926052853269,0.0925076604983,0.0919951301481,0.0928330765936,0.0928818890079,0.0939476267201,0.0935896690152,0.0939394913177,0.0932398467127,0.0932642529199,0.0934757733819,0.094476427875,0.0955340301848,0.0957455506467,0.0964207890445,0.0960872375468,0.0969658610042,0.097917703083,0.0983895564213,0.0990973364286,0.0998132518383,0.1003664592,0.10056984426,0.101838967032,0.102790809111,0.104434160392,0.105101263387,0.10579277259,0.106484281792,0.107118843178,0.107265280421,0.108127633074,0.10941302665,0.109217776993,0.110031317231,0.109681494929,0.110462493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m <- 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ycorr <- 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altd  <- c(228)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('Callithrix_jacchus-male-liver-H3K4me3-ERR572279.50mers.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) : 228',bty='n')
dev.off()