# R script for Peak Model
#  -- generated by MACS
p <- c(0.0429939753284,0.0501353161687,0.0572948632828,0.0644947442955,0.0716450482245,0.0716559719887,0.0716548516026,0.0716330040742,0.0716498098653,0.0716736180694,0.0716402865837,0.0716358050394,0.0716355249428,0.0716640947878,0.0716870627023,0.0717016277213,0.0716817408684,0.0716926646327,0.0716682962355,0.0716996670456,0.0717892979316,0.0717965804411,0.0718139464252,0.0716954655978,0.0717629688588,0.0718013420819,0.0717926590898,0.0717551261563,0.0717245956358,0.071704708783,0.0715943507546,0.0716795000963,0.0716646549808,0.0717461630677,0.0716823010615,0.0716876228953,0.0716814607719,0.0716299230125,0.0715937905616,0.0716355249428,0.0716498098653,0.0715495353116,0.0715374911613,0.0715049999651,0.0714923956218,0.0714652262595,0.0714641058734,0.0715142431503,0.0714960368765,0.0715111620886,0.0715190047911,0.0714845529193,0.0714968771661,0.0714439389241,0.0715120023781,0.0715181645015,0.0715344100996,0.071563260041,0.0715943507546,0.0715153635363,0.0716192793448,0.0716778195172,0.0716498098653,0.0717380402687,0.0715828667973,0.0715450537673,0.0715842672799,0.0715750240948,0.0715797857356,0.0716344045568,0.0715565377246,0.071510881992,0.0715753041913,0.0715484149255,0.0715610192689,0.071593510465,0.0715895891138,0.0715750240948,0.0716251613717,0.0715685818749,0.0715954711407,0.0716055546153,0.0715820265078,0.0715957512372,0.0717173131263,0.0717016277213,0.0716484093827,0.0717114310994,0.0716764190346,0.0717307577592,0.0717584873146,0.0717920988968,0.0718329929885,0.0718523196483,0.0718145066183,0.0718873317131,0.0718688453429,0.0718103051705,0.0718514793588,0.0718391551119,0.0718119857496,0.0718696856325,0.0718184279695,0.0717640892449,0.0717758532987,0.0717215145741,0.0716946253083,0.0717167529333,0.0716708171042,0.071749524226,0.0717013476247,0.0717072296516,0.0717758532987,0.0718419560771,0.0718660443777,0.0718660443777,0.0719478325612,0.0719511937194,0.0719663189314,0.0720147756291,0.0720604313617,0.0720621119408,0.0719912475216,0.0720150557257,0.0720366231576,0.0720027314788,0.07197528202,0.0720242989108,0.0721604258189,0.0720934827509,0.0722270887903,0.0722413737128,0.0723321249848,0.0723660166636,0.0723971073771,0.0724954212552,0.072582811369,0.072567125964,0.0725382760226,0.0725682463501,0.072462930059,0.0724962615448,0.0724777751745,0.0724503257157,0.0725237110036,0.0725760890526,0.0726094205383,0.0726564767534,0.072687007274,0.072762633334,0.0728645884668,0.0729432955886,0.0730037964366,0.0731570092323,0.0731486063368,0.0731805373399,0.073249160987,0.0733214258888,0.0733555976641,0.0733331899426,0.0734202999599,0.0733522365059,0.0734141378365,0.0733522365059,0.0733774451925,0.0734236611181,0.0734768794567,0.0735074099772,0.0734768794567,0.073474358588,0.0734348649789,0.0735987214423,0.0736578218077,0.0736777086606,0.0738087938313,0.07384912773,0.0738317617458,0.0738513685022,0.0739359576508,0.0740048613944,0.0740362322045,0.0740950524734,0.0741510717771,0.074283837527,0.0742698327011,0.0742325798641,0.0742916802295,0.0743149282406,0.0744163231803,0.0745342438147,0.074642921264,0.0746622479237,0.0746829750661,0.0746600071516,0.0746588867655,0.0748064976309,0.0749232978792,0.0749969632636,0.0749863195959,0.0750120884756,0.075093316466,0.0751546576036,0.0752442884896,0.0753420421746,0.0754809700479,0.0754636040637,0.0754787292757,0.0755952494275,0.0757588257944,0.0758610610237,0.0758913114477,0.0759809423337,0.0760083917925,0.0760546077181,0.0760249174871,0.0761705676769,0.0762985717859,0.0764190132889,0.0765120053331,0.0766083585356,0.0767229180117,0.0767909814657,0.0769010593976,0.0770892842581,0.0772539810111,0.0773455725727,0.0774287612388,0.0774192379571,0.0774346432657,0.0774531296359,0.0775043872988,0.0775774924902,0.0777122189157,0.0776996145723,0.0776657228936,0.0777068970818,0.0777850440105,0.0779474999914,0.0780833468029,0.0782102305259,0.0783365540558,0.0784093791507,0.0785272997851,0.0786258937596,0.0787903104161,0.0789578081343,0.0790314735187,0.0791872071831,0.0792866414472,0.0793975596686,0.0794843895894,0.0795995092586,0.0796563688519,0.0798325495621,0.0800300176078,0.0801199285903,0.0803232786629,0.0803885411517,0.080513464199,0.0806621954505,0.0807663913554,0.0809397711005,0.081126875575,0.0812501180432,0.0813770017661,0.0814683132312,0.0815388975539,0.0816797861028,0.0818178736865,0.0819509195329,0.0821926428285,0.0823452954312,0.0824366068963,0.0826844923154,0.0828909234496,0.0831379685791,0.0834077015266,0.0835076959838,0.0836849970801,0.0838693005894,0.0840048673044,0.0840838545227,0.0843538675667,0.0844415377771,0.0845530161915,0.0846258412863,0.0846622538338,0.0848840902766,0.0850443054853,0.0852286089946,0.0853563330071,0.085610100453,0.085646793097,0.0857616326696,0.0858901969717,0.0861153945727,0.0863114621358,0.0866024824187,0.0867758621638,0.0868702546906,0.0871629555526,0.0874654597928,0.0878458308651,0.0882774596004,0.0887228130651,0.0892199843858,0.089679622773,0.0900241414909,0.0904731362104,0.0909495803887,0.0912904578519,0.0916097678832,0.0919374808101,0.092153715322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m <- 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ycorr <- 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altd  <- c(250)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('A549-100nM-Dex-1h-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) : 250',bty='n')
dev.off()