# R script for Peak Model
#  -- generated by MACS
p <- c(0.0429556552869,0.0501237550974,0.0572872511186,0.0644256820652,0.0715761340171,0.0715786916777,0.0715776686135,0.0715464651532,0.0715477439836,0.0715676937368,0.071587131958,0.0716001760274,0.0715733205903,0.0715822724027,0.0716155219915,0.0715786916777,0.0716144989272,0.0715751109528,0.0715293288267,0.071606314413,0.0716193584825,0.0716231949735,0.0716111739683,0.071564624544,0.0715421171301,0.071564368778,0.0716226834414,0.0716866249583,0.071700947858,0.0716367505751,0.0717114342668,0.0716771616138,0.071678184678,0.0716600252872,0.0716472369839,0.0716344486805,0.0715753667189,0.0715582303923,0.0715689725672,0.0715572073281,0.0715063098806,0.0714876389577,0.0714858485952,0.0715446747907,0.0715587419245,0.0715180751197,0.0714618065848,0.0714579700938,0.0714751064204,0.0714994041968,0.0714369972763,0.0714229301426,0.0715293288267,0.0715045195181,0.07157204176,0.0716155219915,0.0716129643308,0.0716075932434,0.0716091278398,0.071602477922,0.0716216603771,0.071651585007,0.0715390479373,0.071530351891,0.0714126994999,0.0714666661401,0.0714794544435,0.0714728045258,0.0714694795669,0.0714311146567,0.0714298358264,0.0714439029601,0.071481244806,0.0715630899476,0.0716277987627,0.0715551611995,0.0715705071636,0.0715582303923,0.0715899453847,0.0716267756984,0.0716088720737,0.0716270314645,0.0716081047755,0.0716104066701,0.0716185911843,0.0716157777575,0.0716058028809,0.0715357229784,0.0715224231429,0.0715536266031,0.0716359832769,0.0716265199324,0.0717183399506,0.0717390570021,0.0717569606269,0.0718262732312,0.0718904705141,0.0719707810594,0.0719582485221,0.0719891962162,0.0719874058538,0.0720152843551,0.0719546677971,0.0719953346019,0.072026282296,0.0719948230697,0.0719912423448,0.0720613222473,0.0720984083271,0.07211707925,0.0720925257075,0.0720953391343,0.0721730920188,0.0721966224971,0.0721068486073,0.0721582575869,0.072101989052,0.0721035236484,0.0721165677179,0.0720940603039,0.0721239849339,0.0721741150831,0.072139586664,0.072064135674,0.0722042954791,0.0722163164843,0.072275909978,0.0723344804075,0.0723679857623,0.0724053276082,0.0725060994388,0.0725045648424,0.0725728543825,0.0726206826371,0.0725173531458,0.0725984309892,0.0725971521589,0.0725838523234,0.0726350055369,0.0725887118787,0.0725910137733,0.0725912695394,0.0726030347785,0.0726554668223,0.0727674923599,0.0727695384885,0.0727969054577,0.0728455010105,0.0728137860182,0.0729061175686,0.0729212077666,0.0729787551318,0.0730125162527,0.0730462773736,0.0730897576051,0.0731130323173,0.0732058753998,0.0731969235874,0.0732631669989,0.0732736534077,0.0733171336392,0.0733690541509,0.073410999786,0.0734764758993,0.0735340232645,0.0735782707942,0.0735882456708,0.0735979647814,0.0736058935295,0.0737309631366,0.0737396591829,0.0738186908978,0.0738220158566,0.0738481039955,0.0739087205535,0.0739199742605,0.074042741973,0.0741655096854,0.0742642353875,0.0742527259145,0.0743921184213,0.0744586175989,0.0745496703189,0.0745865006327,0.0746044042574,0.0746867609312,0.0747381699108,0.0747954615099,0.0748704009677,0.0749693824359,0.0749563383664,0.0749801246107,0.0750977770018,0.0752028968556,0.0753213165449,0.0753942098742,0.0753844907636,0.0755052123475,0.0756113552655,0.0757323326155,0.0758448696853,0.0759366897035,0.0759709623566,0.0760274866575,0.0760533190303,0.0761586946502,0.0763142004193,0.0763088293319,0.0763630517382,0.0764062762036,0.0764308297461,0.0764978404558,0.076615748613,0.0766791785978,0.0768193384028,0.0769566847811,0.076990445902,0.0771083540592,0.0771367440927,0.0771891761365,0.0773579817412,0.0774490344612,0.0774559401451,0.0775902173305,0.0776191188962,0.07764878776,0.0777881802669,0.0779004615705,0.0780669652805,0.0782477918903,0.0783291254998,0.0784112264075,0.0785411555699,0.0786575291306,0.078817894455,0.0789235258409,0.0790329937179,0.0790271110983,0.0790964237026,0.0791117696667,0.0792350489113,0.0793846720608,0.0795304587193,0.0796660147352,0.0797793191031,0.0798795794016,0.079945567047,0.0802310019785,0.0803338199377,0.0804949525602,0.0806443199437,0.0807087729928,0.0808215658286,0.0808870419419,0.080993440626,0.0811430637755,0.0812934542233,0.0813451189689,0.0814957651827,0.0816407845431,0.0817446255665,0.0819057581891,0.0820932347167,0.0823275164346,0.082510644939,0.082650804744,0.0828579752588,0.0829894390175,0.0831001857248,0.0831687310309,0.0833096581341,0.0834963673635,0.0836879361481,0.0837830811253,0.0838587878813,0.0839626289047,0.0840759332727,0.0842114892885,0.0844675111222,0.0846774950637,0.0848468122004,0.0850309637691,0.0850862092397,0.0851245741498,0.0853366042199,0.0855949279481,0.0857783122186,0.0859790885817,0.0860852314997,0.0862210432816,0.0863236054747,0.0865075012773,0.0866520091055,0.0868678756666,0.087028496757,0.0871016458523,0.0872962838298,0.0874955255964,0.0876863270829,0.0879482315361,0.0882917253649,0.0885546528824,0.0889290944053,0.089291003391,0.0896720948317,0.090153702337,0.0905312130528,0.0908984931258,0.0913159033481,0.0916972505549,0.0920085178592,0.0922192690989,0.0924873119377,0.0927548432444,0.09290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m <- 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ycorr <- 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altd  <- c(4, 258)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('A549-100nM-Dex-3h-H3K27ac.pooled.sorted.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) : 4,258',bty='n')
dev.off()