# R script for Peak Model
#  -- generated by MACS
p <- c(0.0424543264101,0.0491580152588,0.0561034065687,0.0631980846928,0.0701292582109,0.0696813977682,0.0695889821213,0.0700226247721,0.0704775941108,0.0704136140475,0.0706482076127,0.0707477321556,0.0709112367616,0.0709112367616,0.0709325634494,0.0709041278657,0.0705984453413,0.0704278318394,0.0699799713966,0.0698733379579,0.0690984683031,0.0696458532886,0.0692477551173,0.069439695307,0.0695818732254,0.0697524867273,0.0700084069803,0.0699017735416,0.0697595956233,0.0693899330356,0.0696600710804,0.0694183686193,0.0697880312069,0.069439695307,0.0693330618683,0.0697240511437,0.069525002058,0.0695107842662,0.0696031999131,0.0702145649619,0.0700581692517,0.0697595956233,0.07020034717,0.070036842564,0.0700652781476,0.0695036753703,0.0694183686193,0.0690487060317,0.0691979928459,0.0688709836338,0.0691624483663,0.069020270448,0.0686221722767,0.0689491814888,0.0687359146114,0.068679043444,0.0687501324032,0.0690700327194,0.069020270448,0.0687714590909,0.0690060526562,0.0690060526562,0.0684231231911,0.0682311830013,0.0680534606034,0.0683235986482,0.0682240741054,0.0685581922135,0.0686079544849,0.0690629238235,0.0678828471014,0.0682880541686,0.0687785679869,0.0685724100053,0.0691624483663,0.0693117351805,0.0697169422478,0.069780922311,0.0693188440765,0.0688923103215,0.0699017735416,0.0692832995969,0.069105577199,0.0694254775152,0.0691482305745,0.0685226477339,0.0681387673544,0.0680961139789,0.0683804698156,0.0684373409829,0.0678828471014,0.0683520342319,0.0684089053992,0.0681103317708,0.0679894805402,0.0685013210461,0.0689847259684,0.0686079544849,0.0684444498788,0.0682809452727,0.0685653011094,0.0682169652095,0.0683235986482,0.0685439744216,0.0688212213623,0.0683804698156,0.0678686293096,0.0675060756179,0.0676056001607,0.0678686293096,0.0677264513913,0.0678828471014,0.0676198179525,0.0676340357444,0.0675274023056,0.0677406691831,0.0678757382055,0.0678188670382,0.0681316584585,0.0680605694993,0.0682667274809,0.0684799943584,0.0686719345481,0.0684017965033,0.0683235986482,0.0679255004769,0.0677122335995,0.0681032228748,0.0684017965033,0.0682454007932,0.0681885296258,0.0681174406667,0.0675202934097,0.0676269268485,0.0672075019894,0.0679255004769,0.0678117581423,0.0678970648933,0.0670084529038,0.067413659971,0.0676127090566,0.0672999176363,0.0679823716443,0.0681814207299,0.0681245495626,0.0680747872912,0.0683520342319,0.0682667274809,0.0688425480501,0.0684017965033,0.0681316584585,0.068430232087,0.0685581922135,0.068600845589,0.0689207459052,0.0687501324032,0.0688141124664,0.0691766661581,0.0692193195336,0.0692193195336,0.0693686063479,0.0692335373255,0.0691126860949,0.0686861523399,0.0690131615521,0.0692619729091,0.0694254775152,0.0694823486825,0.0690273793439,0.0694112597234,0.0696245266008,0.0700084069803,0.069610308809,0.0700155158762,0.0697027244559,0.069361497452,0.0693757152438,0.0687572412991,0.0693899330356,0.0692904084928,0.0692975173887,0.0695036753703,0.0701079315231,0.0703496339843,0.0708614744902,0.0709894346167,0.0709467812412,0.0716861064165,0.071302226037,0.0714586217472,0.0717571953756,0.0715297107063,0.0713662061003,0.070626880925,0.0703993962557,0.0708756922821,0.0710960680555,0.0710178702004,0.0708543655943,0.0706126631332,0.0703993962557,0.0704847030067,0.0706908609882,0.071643453041,0.0719988978368,0.0714444039553,0.0714159683717,0.0711884837024,0.0716150174573,0.0717216508961,0.071728759792,0.0722548180898,0.0719704622531,0.0719135910858,0.0721268579633,0.0730083610568,0.0733993503322,0.0739040819423,0.0742595267381,0.0744656847196,0.0749917430174,0.0747358227644,0.0751197031439,0.074941980746,0.0743306156972,0.0740178242769,0.0737476862321,0.0739751709014,0.0742453089462,0.0744799025114,0.0739751709014,0.0741528932993,0.0738045573994,0.0737903396076,0.0740036064851,0.0742950712176,0.0744372491359,0.0744656847196,0.0739609531096,0.073840101879,0.0742026555707,0.0741671110911,0.074600753742,0.0749277629542,0.0749064362664,0.0747784761399,0.0745652092624,0.0742879623217,0.0743163979054,0.0746647338053,0.0749704163296,0.0747073871808,0.0752476632704,0.0752547721663,0.0754751479397,0.0755888902743,0.0758519194232,0.0763139976578,0.0766765513495,0.076804511476,0.0767618581005,0.0769893427698,0.0773376786697,0.0773376786697,0.0776007078185,0.0778353013838,0.0783044885142,0.0783613596816,0.0790295958977,0.0788092201243,0.0785959532468,0.0789585069385,0.0782191817632,0.07865993331,0.0786314977264,0.078830546812,0.0786812599978,0.0788660912916,0.0781125483245,0.0788163290202,0.0792641894629,0.0788945268753,0.0797191588015,0.0795556541954,0.0796907232178,0.0795769808832,0.079761812177,0.0799039900953,0.0809063444195,0.0807144042297,0.0806575330624,0.0814608383009,0.0809632155868,0.0815816895315,0.0820793122456,0.0821077478293,0.0822214901639,0.0826906772944,0.0824916282087,0.0826480239189,0.0833944579901,0.0843968123142,0.0853778399506,0.085939442728,0.0872261528887,0.0885910609046,0.0897498109389,0.0904322649468,0.0909085609732,0.0919535686729,0.0924938447625,0.0927924183909,0.0936028325254,0.0939227328416,0.0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m <- 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ycorr <- 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altd  <- c(282)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('Oryctolagus_cuniculus-male-liver-H3K4me3-ERR572213.50mers.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) : 282',bty='n')
dev.off()