# R script for Peak Model
#  -- generated by MACS
p <- c(0.046855947469,0.0549721375632,0.0627895182767,0.0706728128241,0.0786747522727,0.0787890029184,0.0786923292951,0.0789559846312,0.0792943423124,0.078969167398,0.0785033763043,0.0781254703227,0.0781562301119,0.0779760656323,0.077615736673,0.0776860447626,0.0776640734846,0.0776289194398,0.0774267836822,0.0772158594134,0.0774267836822,0.0774795147494,0.0775805826282,0.0776684677402,0.0776772562514,0.0775322458166,0.0777343815742,0.0777124102962,0.0777080160406,0.0780331909551,0.0781738071343,0.0780244024439,0.0778925747758,0.0778266609418,0.0778925747758,0.0779409115874,0.077945305843,0.0774707262382,0.0771103972789,0.0766402119297,0.0768071936425,0.0765830866069,0.0765171727729,0.0768027993869,0.0767940108757,0.0764995957505,0.0767456740641,0.0769170500325,0.0769082615213,0.0770576662117,0.0768687132209,0.0771675226017,0.0769961466333,0.0764556531945,0.0762491231812,0.0767940108757,0.0761612380692,0.0764336819164,0.0765786923513,0.0760689587016,0.0756427159083,0.0752735984379,0.0755504365407,0.075822880388,0.0759591023116,0.0756163503747,0.075713023998,0.0754493686619,0.0753966375947,0.07580090911,0.0758843999664,0.0758712171996,0.07580090911,0.0756778699531,0.0755020997291,0.0752164731151,0.0751725305591,0.074711133721,0.0745265749858,0.0746320371202,0.0747638647882,0.0748912982006,0.0745529405194,0.0745002094522,0.0744870266854,0.074557334775,0.0742014000714,0.0742409483718,0.0741530632597,0.0737136376997,0.0739860815469,0.0740124470805,0.0742014000714,0.0740871494257,0.0739948700581,0.0744299013626,0.0747067394654,0.0749000867118,0.0748473556446,0.0747726532994,0.0746627969094,0.0744562668962,0.0739553217577,0.0738190998341,0.0741354862373,0.0736609066325,0.0732390580948,0.0734543766193,0.0735730215205,0.0739069849461,0.0740080528249,0.0740607838921,0.074403535829,0.0746847681874,0.0743991415734,0.0744123243402,0.0744518726406,0.0742233713494,0.0744430841294,0.0746540083982,0.0743464105062,0.0743859588066,0.0742585253942,0.0738674366457,0.0738410711121,0.0738894079237,0.0740256298473,0.0737531860001,0.0734719536417,0.0728611521132,0.0727952382792,0.0727073531672,0.072742507212,0.0730588936152,0.0727161416784,0.0725403714543,0.0727908440236,0.0733225489512,0.0732873949064,0.0731907212832,0.0728919119024,0.07331376044,0.073247846606,0.0731072304268,0.0732170868168,0.0732566351172,0.0731204131936,0.0732566351172,0.0735466559869,0.0740300241029,0.074293679439,0.0736081755653,0.0737883400449,0.0738015228117,0.0736828779105,0.0733620972516,0.0735774157761,0.073137990216,0.0732214810724,0.0731511729828,0.0731292017048,0.0732961834176,0.0731951155388,0.0730764706376,0.0731775385164,0.0734851364085,0.0732873949064,0.0737443974889,0.0734324053413,0.0731643557496,0.073291789162,0.0733093661844,0.07309404766,0.0728347865796,0.0729270659472,0.0727776612568,0.0729885855256,0.0724964288983,0.0725711312435,0.0724700633647,0.0719251756703,0.0720174550379,0.0722635333515,0.0726721991224,0.0728611521132,0.0727820555124,0.0724085437863,0.072786449768,0.0724788518759,0.0726238623107,0.0730149510592,0.0735202904533,0.0732170868168,0.0729534314808,0.072698564656,0.0730237395704,0.0733313374624,0.0729797970144,0.0729138831804,0.0725931025215,0.0725887082659,0.0719866952487,0.0717977422578,0.0719207814147,0.0721185229167,0.0718460790694,0.0718021365134,0.0719998780155,0.0721492827059,0.0726546221,0.0727512957232,0.0725755254991,0.0729138831804,0.073072076382,0.073050105104,0.0731643557496,0.0729314602028,0.0730588936152,0.0732522408616,0.0735378674757,0.0732434523504,0.0735334732201,0.0735246847089,0.0734499823637,0.0734807421529,0.0739728987801,0.0744518726406,0.0743771702954,0.0745617290306,0.0743903530622,0.074491420941,0.074293679439,0.0743551990174,0.0742848909278,0.0740607838921,0.0739157734573,0.0736081755653,0.0736828779105,0.0733972512964,0.0732961834176,0.0740168413361,0.074359593273,0.0744430841294,0.0744958151966,0.074799018833,0.0747418935102,0.0751593477923,0.0751769248147,0.0754933112179,0.0752340501375,0.0751066167251,0.0752604156711,0.0753395122719,0.0756295331415,0.0757393895316,0.0760557759348,0.0757086297424,0.0760997184908,0.0757877263432,0.0765435383065,0.0765391440509,0.0766314234185,0.0767588568309,0.0767544625753,0.0770752432341,0.0767544625753,0.0770752432341,0.0771499455793,0.0772905617586,0.0772510134582,0.0772378306914,0.0772905617586,0.0775102745386,0.077439966449,0.0774311779378,0.0776289194398,0.0779189403094,0.0778618149866,0.0782792692687,0.0783188175691,0.0785868671607,0.0786352039723,0.0787758201516,0.0786220212055,0.0790043214428,0.0792503997564,0.079100995066,0.0786659637615,0.078793397174,0.0787758201516,0.0790043214428,0.079254794012,0.078969167398,0.0792723710344,0.0784682222595,0.0785385303491,0.0785209533267,0.0791141778328,0.079232822734,0.0797689219173,0.0795931516933,0.0795843631821,0.0801204623653,0.0805906477146,0.0819221071616,0.0823000131432,0.0833897885322,0.0837237519578,0.0842466683743,0.0847739790463,0.0854638771756,0.0859648223141,0.0862592374393,0.086746999811,0.086940347057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m <- 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ycorr <- 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altd  <- c(292)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('Mus_musculus_domesticus-male-liver-H3K4me3-ERR572240.50mers.unique.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) : 292',bty='n')
dev.off()