# R script for Peak Model
#  -- generated by MACS
p <- c(0.0190089384131,0.0221038426441,0.0250888686184,0.0281654598066,0.0313885553372,0.0314068683799,0.0310955466526,0.0316449379362,0.0315350596795,0.0317914422785,0.0319013205352,0.0321210770486,0.0325422770328,0.03252396399,0.0325605900755,0.0324690248616,0.0328169726746,0.0327986596318,0.0334213030865,0.0335311813433,0.0338608161134,0.0335311813433,0.033549494386,0.0334396161293,0.033384677001,0.0336044335144,0.0331099813592,0.0327620335462,0.0319928857491,0.0318830074924,0.0316449379362,0.0321577031342,0.0319013205352,0.0322675813909,0.0321577031342,0.0319013205352,0.0322126422626,0.0325422770328,0.0326704683323,0.0328352857173,0.0324140857332,0.0326155292039,0.0328902248457,0.0330001031024,0.0336776856856,0.0343186421831,0.0343186421831,0.0344651465254,0.0347215291244,0.0349962247662,0.0348314073811,0.0346299639105,0.0346849030388,0.0346482769533,0.0344834595682,0.0342270769692,0.0342087639264,0.0337509378567,0.0334762422149,0.0334029900437,0.0340073204557,0.0340073204557,0.0338425030706,0.0339157552418,0.0338791291562,0.0340622595841,0.0338241900279,0.0345200856538,0.0346849030388,0.0347215291244,0.0347215291244,0.035014537809,0.0349779117234,0.0352342943225,0.0357836856061,0.0355822421354,0.0361133203762,0.0357287464777,0.0360766942907,0.035618868221,0.0355456160498,0.0356371812638,0.0359485029912,0.0361499464618,0.0358203116917,0.0357653725633,0.0361133203762,0.0364063290608,0.0363880160181,0.037340294243,0.0378164333554,0.0375600507564,0.0373586072858,0.0375783637992,0.0378164333554,0.0383658246391,0.0386038941953,0.0391532854789,0.0396477376342,0.0390800333078,0.0390800333078,0.0392997898212,0.039574485463,0.0392448506928,0.0395378593774,0.0395012332919,0.0397209898053,0.0395012332919,0.0392631637356,0.0399956854471,0.0401055637038,0.0404535115168,0.0406000158591,0.0409845897576,0.0408197723725,0.0407648332442,0.0401421897894,0.0401971289178,0.0404535115168,0.0399590593615,0.0399407463188,0.0397209898053,0.0397942419765,0.0393730419924,0.0394279811207,0.0395195463347,0.0395195463347,0.0397942419765,0.0397393028481,0.0402154419606,0.0401971289178,0.0402154419606,0.0403436332601,0.0407282071586,0.0410578419288,0.0408747115009,0.040783146287,0.0406366419447,0.0406183289019,0.0403070071745,0.0400689376183,0.0406366419447,0.0410578419288,0.0412043462711,0.0410761549716,0.0415339810412,0.0423214418811,0.042669389694,0.0429807114214,0.0434385374911,0.0435484157478,0.0431638418493,0.0424679462234,0.0425778244801,0.0427792679508,0.0424313201378,0.0423763810094,0.0424313201378,0.0425961375229,0.0428891462075,0.0434019114055,0.0439146766036,0.0454163461121,0.0455445374116,0.0457276678395,0.0468447634495,0.0467531982356,0.0464235634654,0.0464785025938,0.0466433199789,0.0472659634336,0.0472842764764,0.0464785025938,0.0468081373639,0.0463503112943,0.0464235634654,0.0467715112784,0.0472659634336,0.0474307808187,0.0472476503908,0.047064519963,0.0473575286476,0.0477604155889,0.0477604155889,0.0483464329581,0.0481449894874,0.0481266764446,0.0475955982038,0.0475040329898,0.0484196851292,0.0483098068725,0.0479801721023,0.0479618590595,0.0476322242894,0.0479618590595,0.0481266764446,0.0485295633859,0.0490606416268,0.0494269024825,0.0491155807551,0.049298711183,0.0502143633223,0.0505623111353,0.0509102589483,0.0505439980925,0.0506905024348,0.0508003806915,0.051020137205,0.0516427806597,0.0518259110876,0.0523203632429,0.0521555458578,0.0521555458578,0.052997945826,0.0535839631952,0.0538952849226,0.0541699805644,0.0542432327355,0.0540417892649,0.0538403457942,0.054115041436,0.0544263631634,0.0554335805167,0.0551405718321,0.0553603283455,0.0559097196291,0.0555983979018,0.0559829718003,0.0560012848431,0.0565689891695,0.0567338065546,0.0572831978382,0.0568803108969,0.0581255978064,0.0591328151597,0.0591511282025,0.0603048498981,0.0610373716095,0.061861458535,0.0626122932892,0.0631983106584,0.0627404845888,0.0631799976156,0.062978554145,0.062978554145,0.0634180671719,0.0638758932416,0.0638758932416,0.0642787801829,0.0643337193112,0.0646816671242,0.0660917714188,0.0668975453014,0.0673736844139,0.068051266997,0.0676850061413,0.0679047626547,0.0682160843821,0.0683259626388,0.0690401713075,0.0696261886767,0.0691866756498,0.0697543799762,0.0699924495325,0.0688387278369,0.069772693019,0.0699008843185,0.0706883451584,0.0709447277574,0.0709630408002,0.0702122060459,0.0706517190728,0.0699008843185,0.0710179799285,0.0725562755227,0.0728859102928,0.0731239798491,0.0731056668063,0.0740030059028,0.0748820319566,0.0761456319089,0.0766950231926,0.0783615100862,0.0780135622732,0.0777571796742,0.0785995796424,0.0790940317977,0.0796800491669,0.0802294404505,0.0805773882634,0.0810169012903,0.0820424316864,0.0813648491033,0.0821889360287,0.0829580838258,0.0832694055531,0.0835257881522,0.084313248992,0.0844048142059,0.0848077011473,0.0859247967573,0.0859431098001,0.0869137010678,0.0866206923832,0.0879026053783,0.0889098227316,0.0899170400849,0.0906495617964,0.091455335679,0.0926823095457,0.0930668834443,0.0935796486423,0.094641805124,0.09669286591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m <- 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ycorr <- 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altd  <- c(228)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('A549-100nM-Dex-10h-p300.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) : 228',bty='n')
dev.off()