# R script for Peak Model
#  -- generated by MACS
p <- c(0.0425779593157,0.0496791041741,0.0567557868649,0.0638702747237,0.0710167857837,0.0710479194515,0.0711413204549,0.0712195993911,0.0712244918246,0.0712836457934,0.0712938754271,0.0712138174242,0.0713272329283,0.0712809771933,0.0712680789595,0.0712622969926,0.0712849800935,0.0712409481919,0.0712498435255,0.0712195993911,0.0712498435255,0.0713521398626,0.071143989055,0.0711942476902,0.0711533291553,0.0711995848904,0.0710955094866,0.0709465126478,0.0709144894467,0.0708397686439,0.0708353209771,0.0708126378763,0.0709407306809,0.0708998121461,0.0708344314437,0.0707245740731,0.0707308008066,0.0707410304403,0.0708215332099,0.0709100417798,0.0707930681422,0.070867788945,0.0708468849109,0.0708682337116,0.0709994398831,0.0709691957486,0.070998105583,0.071051477585,0.070943399281,0.070895809246,0.0708811319454,0.0707472571739,0.0707018909723,0.070620943436,0.0704368100293,0.0703976705612,0.0704110135617,0.0704919610979,0.0705342139328,0.0704448158296,0.0704194641286,0.0704812866976,0.0704368100293,0.0704995221316,0.0705813592012,0.0706191643692,0.0705560075003,0.0704599378968,0.0704915163313,0.0705511150668,0.0706351759698,0.0705875859348,0.0707365827735,0.070703670039,0.0706258358695,0.0705773563011,0.0705729086342,0.0706458503702,0.0705840278013,0.0705800249012,0.0705711295675,0.0704715018305,0.0703349584589,0.0703340689255,0.0703932228944,0.0704617169635,0.0703781008271,0.0703385165924,0.0702869236572,0.0702544556893,0.0702887027239,0.0703732083936,0.0704172402952,0.0703665368934,0.0704127926284,0.070503080265,0.0706093795022,0.0704434815295,0.070567571434,0.0706285044696,0.0705426644998,0.0704964087648,0.0704839552977,0.0706351759698,0.0706107138023,0.0705057488651,0.0705204261657,0.0706729811379,0.0706387341033,0.0706863241384,0.0706898822718,0.0707543734408,0.0707761670083,0.0706738706712,0.0707085624725,0.070776611775,0.0707192368729,0.070842437244,0.0708811319454,0.0707379170736,0.0708459953775,0.0708740156785,0.0708571145446,0.0709038150463,0.0709856521159,0.0709167132801,0.0709683062153,0.0709669719152,0.0708926958792,0.0710368002844,0.0710835007861,0.0710550357184,0.0710750502192,0.0710906170531,0.0709745329488,0.0710861693862,0.0711235297876,0.0711502157886,0.071235166225,0.0712645208261,0.0712293842581,0.0712774190599,0.0713828287637,0.071500247168,0.0715273779356,0.0715545087033,0.0716439068065,0.0716336771728,0.0717075084422,0.0717083979755,0.0716545812069,0.0717546537106,0.0717306363097,0.0717350839765,0.0718845255819,0.0717973513121,0.0717826740116,0.0718631767812,0.0718529471475,0.0719036505493,0.0720762200223,0.0721131356569,0.0722198796608,0.0722158767607,0.0722474551951,0.0724849606038,0.0726250621089,0.0726232830422,0.072673986444,0.0726775445775,0.0725859226408,0.0726477452097,0.0727985211152,0.0728407739501,0.0728723523846,0.0728581198507,0.0728287652496,0.072922166253,0.0729248348531,0.0729857678887,0.0730591543913,0.0730720526251,0.0730102300562,0.0730840613256,0.073142325761,0.0731747937289,0.0733451393684,0.073424307838,0.0734990286407,0.0735506215759,0.0736658161468,0.0738250426192,0.0739033215554,0.0740358620269,0.0741386031306,0.0741688472651,0.0741697367984,0.0741563937979,0.0742938267029,0.0744188061408,0.0746047186142,0.0746558667828,0.0747239160852,0.0747790671539,0.0748115351218,0.0749658691607,0.0750432585635,0.0751811362352,0.0752772058387,0.0754075224768,0.0754573363453,0.0754177521105,0.0755298333146,0.0756761615532,0.0756757167865,0.0757673387232,0.0758976553613,0.0759141117285,0.0759981726316,0.0759670389638,0.0759332366959,0.0761169253359,0.076083123068,0.0760840126014,0.0762792651752,0.0763548755113,0.0763806719789,0.0765559100519,0.0767253661581,0.076914836765,0.0770842928711,0.0771701328409,0.0773622720479,0.0774263184502,0.0775032630864,0.0776042251234,0.0777523324288,0.0778363933318,0.0778363933318,0.077886651967,0.0779378001355,0.0780512156396,0.0781286050424,0.0783118489158,0.0784528399542,0.0785440171242,0.0785747060253,0.0787076912635,0.0789251821714,0.0792004927481,0.079353492487,0.0795087160593,0.0797831371026,0.0798498521051,0.0800740145132,0.0802074445181,0.0804409470266,0.0804889818283,0.0805187811961,0.0804783074279,0.0806833448687,0.0807767458721,0.0808194434737,0.0810565041156,0.0811868207537,0.0814238813957,0.0815226195993,0.0817841424088,0.0818797672456,0.0820563396187,0.082155522589,0.0822618218262,0.0825126702353,0.0825389114696,0.0825371324028,0.0826683385743,0.0828595882479,0.0829885705859,0.0832723317296,0.0835342993058,0.0836788484777,0.0839323654869,0.0840328827573,0.0843055247338,0.0845795010105,0.0847462885165,0.0849588869909,0.0851830493991,0.0853422758716,0.0855117319777,0.0857479030863,0.0859440451935,0.0860921524988,0.0862598295383,0.0864426286449,0.0866387707521,0.0867988867579,0.0870177119658,0.087379307279,0.0875919057534,0.0879988672682,0.0883760294153,0.0888528192993,0.0893656352846,0.0898820094034,0.0903583545207,0.0909249872747,0.0913613033905,0.0918091834402,0.0923469063597,0.0927600946081,0.0931350329217,0.0935099712354,0.093786171345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m <- 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ycorr <- 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altd  <- c(263)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('A549-100nM-Dex-7h-H3K27ac.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) : 263',bty='n')
dev.off()