# R script for Peak Model
#  -- generated by MACS
p <- c(0.0430501384348,0.0501941148197,0.0573599493679,0.0645471563426,0.071671217512,0.0715913137816,0.0716442591105,0.0715398256635,0.0715570693257,0.071512867262,0.0714460784296,0.0715235534752,0.0714764369898,0.0715228248698,0.0715696984867,0.0715660554595,0.0715580407996,0.0714924663096,0.0714999952325,0.0715233106067,0.0715764988042,0.0715580407996,0.0715823276477,0.0715162674208,0.0715446830331,0.071571884303,0.0715548835093,0.0716520309019,0.0716423161627,0.0717134766278,0.0717669076937,0.0717314488954,0.0717545214012,0.0717778367754,0.0717455352673,0.0716721889859,0.0716697603011,0.0716328442919,0.0716466877954,0.0715842705956,0.0714914948356,0.0714873660715,0.0714232487923,0.0713715178057,0.0713321731117,0.0713557313544,0.0714181485542,0.0714310205837,0.0713768609123,0.0714159627379,0.0715087384978,0.071572855777,0.0716058858904,0.0715551263778,0.0716401303463,0.0716151148927,0.0715847563326,0.0716828751991,0.0716940471493,0.0716284726592,0.0715089813663,0.071407948078,0.0714312634522,0.0714982951531,0.071440249586,0.0715458973755,0.0715369112417,0.0715318110036,0.0716024857317,0.0715730986454,0.0716224009472,0.0716479021378,0.0716284726592,0.0716352729767,0.071624829632,0.0715276822394,0.0714353922164,0.0713756465699,0.071361074461,0.0714113482367,0.0713739464906,0.0713256156627,0.0713035146309,0.071229439744,0.0712070958437,0.0712279825332,0.0713734607536,0.0713506311163,0.0713321731117,0.0713112864223,0.0713069147897,0.0713899758103,0.0713562170914,0.0714387923751,0.0715101957087,0.0715237963437,0.0714577361167,0.0714922234411,0.0715182103686,0.0714812943594,0.0715213676589,0.0714638078287,0.0715563407202,0.0715446830331,0.0715475974549,0.0715417686113,0.0715791703575,0.0715706699606,0.0715291394503,0.0715939853349,0.0716391588724,0.0717132337593,0.071671217512,0.0716644171945,0.0716367301876,0.071723677104,0.0717489354261,0.0718463256872,0.0719038855173,0.071941530132,0.071901213964,0.0719267151546,0.0719918039076,0.0720588356085,0.0721581688175,0.0721047377516,0.0721088665157,0.0720566497922,0.0720668502684,0.0720532496335,0.0720964802232,0.072151854237,0.0721722551894,0.0721530685794,0.0721414108923,0.0721897417201,0.0722322437044,0.0721700693731,0.0722482730242,0.0723442060744,0.0725168855648,0.0725263574355,0.0725902318462,0.0726541062568,0.0726689212342,0.0727429961211,0.0727590254409,0.0729426340129,0.0729168899539,0.0728964890014,0.0728935745796,0.0729300048519,0.0729445769608,0.0729581775957,0.0730380813262,0.0730686827548,0.073099527052,0.0730439101697,0.0732010460773,0.0732471910888,0.0732170753971,0.0732355334017,0.0732865357828,0.073376397121,0.0733924264408,0.0733887834135,0.0734344426881,0.0735549054549,0.0735165322348,0.073665410614,0.0737015980178,0.0737518717935,0.0737873305918,0.0737873305918,0.0738223036531,0.0738164748096,0.0739485952635,0.0739889114315,0.074007855173,0.074001297724,0.0740318991527,0.074040642418,0.0740396709441,0.0741645053436,0.0741955925093,0.0743571000495,0.0743792010813,0.0743775010019,0.0745441087803,0.0746186694041,0.0747758053117,0.0749037970015,0.0750704047798,0.0750861912311,0.0752243833971,0.075298944021,0.0754045918104,0.075535983659,0.0754609372982,0.075482066856,0.0754718663798,0.0755328263687,0.0756532891355,0.0757586940565,0.0757873525374,0.0758587558709,0.0758862000094,0.0760005910642,0.0762155296703,0.0763794658954,0.0765273728007,0.0765657460207,0.0765676889686,0.0766864516561,0.0768632599106,0.0768805035728,0.0769421921672,0.077036425138,0.077115114526,0.0771913752292,0.0772571925877,0.0774053423615,0.0775661212963,0.0776785694032,0.0776807552196,0.0778796645059,0.0780263570688,0.07811573267,0.0781978222168,0.0782631538383,0.0783420860948,0.078438019145,0.0784958218437,0.0785626106761,0.0787236324793,0.0788372949287,0.0789069981829,0.0790116744985,0.0791292228435,0.0792574574018,0.0794597668469,0.079570757743,0.0797439229704,0.0797937110091,0.0799107736172,0.0800193358284,0.0802337886976,0.080334336249,0.0804054967141,0.0804939008414,0.0806099919756,0.080742841035,0.0808419313755,0.0810320973965,0.0811498886101,0.0812535934517,0.0812744801411,0.0814512883957,0.0816353827047,0.081762645789,0.0818355063335,0.0819802559485,0.0821512353595,0.0823188146118,0.0824786220727,0.0827057041029,0.0829500297953,0.0830432912923,0.0831975127781,0.0833813642186,0.0835443289697,0.0837034078251,0.0838467002292,0.0839931499236,0.0841498000942,0.0842624910697,0.0843834395735,0.0845787058326,0.084665652749,0.084857275981,0.0850795006416,0.0852142926489,0.0853410699962,0.0854644471849,0.0856587419701,0.0857962055307,0.0858838810525,0.0859744709961,0.0861940241035,0.0862996718929,0.0863703466211,0.0865877139121,0.0868033811237,0.0870498926325,0.0871861418506,0.0873449778375,0.0875521446523,0.0878824457872,0.0881010274206,0.0883919838615,0.0887271423661,0.089004498172,0.0893374708602,0.0896415421991,0.0899640715426,0.0903958917028,0.0908340264435,0.0911023961157,0.091467184575,0.0918312444288,0.0920750843843,0.0923813415395,0.0925812222998,0.0928860222442,0.09306355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m <- 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ycorr <- 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altd  <- c(4, 260)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('A549-100nM-Dex-7h-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) : 4,260',bty='n')
dev.off()