# R script for Peak Model
#  -- generated by MACS
p <- c(0.020499691305,0.0239651787818,0.0270841175109,0.0308428385435,0.0343882988082,0.0342016956364,0.0347881627478,0.0354279450512,0.0358011513949,0.0364142761023,0.0362809881224,0.0364142761023,0.0365475640822,0.0363609609104,0.0364675912943,0.0364675912943,0.0370807160017,0.0362010153345,0.0363076457184,0.0365475640822,0.0365209064862,0.0363343033144,0.0366541944661,0.0366008792741,0.0364409336983,0.0366808520621,0.0358278089909,0.0362010153345,0.0359344393748,0.0354812602432,0.0354279450512,0.0359610969707,0.0361210425466,0.0366008792741,0.0368941128299,0.0362276729305,0.0362010153345,0.0364142761023,0.0366275368701,0.03676082485,0.0368141400419,0.0365209064862,0.0364675912943,0.0360410697587,0.0360677273546,0.0366275368701,0.0363076457184,0.0363076457184,0.0361743577385,0.0358544665868,0.0353746298593,0.035667863415,0.0355079178392,0.0351347114955,0.0348947931317,0.0348148203438,0.0355878906271,0.0353213146673,0.0352146842834,0.0353479722633,0.035721178607,0.0357744937989,0.0358278089909,0.0360943849506,0.0357744937989,0.0361477001426,0.0363076457184,0.0366008792741,0.0368941128299,0.0372673191735,0.0373472919615,0.0370274008098,0.0365209064862,0.0371073735977,0.0372673191735,0.0370007432138,0.0366808520621,0.0368141400419,0.0374539223454,0.0368141400419,0.0371073735977,0.0369740856178,0.0377204983051,0.0372939767695,0.0373739495574,0.0372140039816,0.0375605527293,0.0375338951333,0.0369207704258,0.0377204983051,0.0371606887896,0.037827128689,0.0374272647494,0.0380403894568,0.0376405255172,0.0381736774367,0.0380670470528,0.0381736774367,0.0381470198407,0.037853786285,0.0381736774367,0.037853786285,0.0387868021441,0.0379604166689,0.0388134597401,0.0390800356999,0.039959736367,0.0396131876194,0.0398531059831,0.0399064211751,0.0404662306906,0.0412126433779,0.0405462034785,0.0413992465497,0.0413459313578,0.0411593281859,0.0407328066503,0.0409993826101,0.0409727250141,0.0405195458825,0.041052697802,0.0406528338624,0.04113267059,0.0408927522262,0.0408660946302,0.0406261762664,0.0401196819429,0.0402529699228,0.0413192737618,0.0416391649135,0.0412126433779,0.0406794914584,0.0410260402061,0.0408927522262,0.0408927522262,0.0404662306906,0.0408927522262,0.0407594642463,0.0403862579026,0.0412126433779,0.0410260402061,0.0414259041457,0.0409993826101,0.0417724528934,0.0420390288531,0.0427854415404,0.0425455231766,0.0433452510559,0.0426521535605,0.0431853054801,0.0438250877835,0.0446248156627,0.0448647340265,0.0444648700869,0.0444648700869,0.044278266915,0.0442516093191,0.0435051966318,0.0440116909553,0.0429453871163,0.0429987023082,0.043238620672,0.0433985662479,0.0433452510559,0.0442516093191,0.0444915276828,0.045451201138,0.045424543542,0.0459310378655,0.0466507929568,0.0466507929568,0.0463042442092,0.0467041081488,0.0467307657448,0.0462775866132,0.0456644619058,0.0455311739259,0.0458244074816,0.0462775866132,0.0458244074816,0.0460376682494,0.0452379403702,0.0448647340265,0.0448114188346,0.0449713644104,0.0460110106534,0.0456644619058,0.0458510650776,0.0461176410373,0.0463842169971,0.0462242714212,0.0467574233408,0.0467574233408,0.0473705480482,0.04755715122,0.0472372600683,0.0477170967959,0.0485701398671,0.0480369879476,0.0493698677463,0.0499829924538,0.050836035525,0.0509160083129,0.0510492962928,0.0515824482123,0.0520889425358,0.051902339364,0.0521422577278,0.0520889425358,0.0513958450405,0.050836035525,0.0503028836055,0.0505694595652,0.0505694595652,0.0501162804336,0.050862693121,0.0509693235049,0.0510226386968,0.0515024754244,0.0515824482123,0.051875681768,0.0529153280111,0.0532885343547,0.0536084255064,0.0539816318501,0.0532085615668,0.0539016590621,0.0545147837696,0.0541682350219,0.0544614685776,0.0549679629012,0.0542482078098,0.0545147837696,0.0552345388609,0.0555277724166,0.0559276363563,0.0560076091442,0.0555011148207,0.0557943483764,0.056247527508,0.0565674186597,0.0569406250033,0.0577136952866,0.057260516155,0.057313831347,0.0581935320142,0.0589399447015,0.0592331782572,0.0595797270049,0.0593131510451,0.0593931238331,0.0601395365204,0.0597396725807,0.060512742864,0.0610725523795,0.0610192371876,0.0609925795916,0.0601395365204,0.0604860852681,0.0608326340157,0.0613391283393,0.0617389922789,0.0628852689058,0.0636583391891,0.063738311977,0.0648046158161,0.0654443981195,0.0673370874337,0.0680035273331,0.0686166520405,0.069203119152,0.0693097495359,0.0696029830916,0.0690698311721,0.0699228742433,0.0689098855963,0.0683767336768,0.0686966248285,0.0689098855963,0.0695496678997,0.0692830919399,0.0697895862634,0.0694430375158,0.0707759173145,0.0708292325065,0.0728018946087,0.0736549376799,0.0742414047913,0.0748811870947,0.0753343662263,0.0757875453579,0.0760541213177,0.0766139308331,0.076773876409,0.0776002618842,0.0768805067929,0.0772537131365,0.0774936315003,0.0787465385112,0.0790930872588,0.0803726518657,0.0816788740685,0.0826918627155,0.0839447697264,0.0844246064539,0.0862639805762,0.0873835996072,0.0880500395066,0.0885831914261,0.0904758807403,0.0910623478518,0.0913822390035,0.0921819668827,0.0923685700546,0.09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m <- 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ycorr <- 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altd  <- c(222)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('A549-100nM-Dex-12h-p300.pooled.sorted.pseudoRep1.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) : 222',bty='n')
dev.off()