# R script for Peak Model
#  -- generated by MACS
p <- c(0.0308042982484,0.0358569947063,0.041226309219,0.0457513089188,0.0509623144041,0.051001891661,0.0507644281199,0.050474194903,0.0511602006884,0.0506456963493,0.0512393552021,0.0511074310126,0.0508435826336,0.0514768187432,0.0514240490674,0.0514768187432,0.0521760169475,0.0526641364487,0.052044092758,0.0525981743539,0.0522024017854,0.0529807545035,0.0529015999898,0.0526245591918,0.0532182180446,0.0539174162489,0.0537195299647,0.0538382617352,0.0542472267227,0.0539174162489,0.0542340343037,0.0540097631816,0.0544055357501,0.0551047339544,0.0548013083186,0.0543923433311,0.0544978826827,0.0537854920594,0.0533369498151,0.0531918332067,0.0529015999898,0.053099486274,0.0529279848277,0.0521892093665,0.052044092758,0.0521364396907,0.0518066292169,0.0522815562991,0.052571789516,0.0537327223836,0.0541021101142,0.0541153025332,0.0539438010868,0.054959617346,0.0548408855754,0.0556456231314,0.0565031303631,0.0564239758494,0.0563580137547,0.0555136989419,0.0552630429818,0.054946424927,0.055487314104,0.0550387718597,0.0554213520092,0.0543131888174,0.0534424891667,0.0534688740046,0.0537986844784,0.0542208418848,0.0540361480195,0.0542868039795,0.0541153025332,0.0542999963985,0.0541416873711,0.0545638447775,0.0552630429818,0.0553026202387,0.0553421974955,0.0556983928072,0.056001818443,0.0554609292661,0.055737970064,0.0558567018346,0.0561997047273,0.0559490487672,0.0557247776451,0.0560282032809,0.0558303169967,0.0550915415355,0.0554213520092,0.0561205502136,0.0563448213357,0.0560941653757,0.0557247776451,0.0557247776451,0.056001818443,0.0554477368471,0.056001818443,0.0563712061736,0.0560413956999,0.0561469350515,0.0554477368471,0.0560413956999,0.0561733198894,0.056806555999,0.0568989029316,0.0569648650264,0.0561997047273,0.0561733198894,0.0561733198894,0.0554081595903,0.0561073577946,0.0558698942535,0.056015010862,0.0560677805378,0.0558567018346,0.0563184364978,0.0565559000389,0.0572419058243,0.0577432177444,0.0579279116097,0.0579015267718,0.0584951856246,0.0589569202878,0.058917343031,0.0587062643278,0.0589437278689,0.0591548065721,0.0587722264225,0.0589701127068,0.0596297336543,0.0595769639785,0.0592207686668,0.0584688007867,0.0585479553004,0.0586007249762,0.0582841069214,0.0585743401383,0.0589569202878,0.0591284217342,0.0589437278689,0.0591284217342,0.0594978094648,0.0597352730059,0.059972736547,0.0606323574945,0.0613579405368,0.0617932903621,0.0616085964968,0.0617669055242,0.0623869492149,0.0623341795391,0.0617800979432,0.0622814098633,0.0624661037286,0.0627299521076,0.0624529113096,0.0625848354991,0.0624265264717,0.0619779842274,0.0618988297137,0.0622550250254,0.0625452582423,0.0628091066213,0.0629542232297,0.063152109514,0.0630861474192,0.0625320658233,0.0627299521076,0.0627431445265,0.0627563369455,0.0626771824318,0.063152109514,0.063415957893,0.0637061911099,0.0633895730551,0.0639700394889,0.064722007369,0.0654343979923,0.0659884795882,0.0665293687652,0.0670042958474,0.0675056077675,0.0675188001864,0.0672285669695,0.0672285669695,0.0677298788896,0.0679145727549,0.0671889897127,0.0666481005357,0.0664106369946,0.0669251413337,0.0659093250745,0.0659620947503,0.0659489023314,0.0667536398873,0.0671626048748,0.0673209139022,0.0678090334033,0.0686137709593,0.0693261615826,0.0690755056225,0.0703024005849,0.0703815550986,0.0706981731534,0.070816904924,0.0702364384901,0.0697747038269,0.0701836688143,0.0707641352482,0.0705002868692,0.070539864126,0.0710543684651,0.0720306074674,0.0723604179411,0.0724659572927,0.0727957677665,0.0732970796866,0.0738775461204,0.0741809717562,0.0742601262699,0.0748405927037,0.0743392807836,0.0743524732026,0.0746295140005,0.0749065547985,0.0752231728533,0.0749725168932,0.0749197472174,0.0749725168932,0.0751440183396,0.0752627501101,0.0756980999355,0.0756189454218,0.0757376771923,0.0755002136512,0.075289134948,0.0760411028282,0.076344528464,0.0767534934515,0.0778616566433,0.0777297324538,0.077927618738,0.0786663941992,0.0788906653214,0.0800911754458,0.0807903736502,0.0809091054208,0.0809486826776,0.0807771812313,0.0805001404333,0.081634688463,0.0819381140989,0.081898536842,0.0817006505578,0.0813444552461,0.0815951112062,0.0823338866674,0.0828483910064,0.0827560440738,0.0826505047222,0.0820304610315,0.0818061899094,0.0822151548968,0.0828483910064,0.0825185805327,0.0821887700589,0.0823866563432,0.0824130411811,0.0829935076149,0.0829803151959,0.0833892801834,0.0836267437245,0.0829803151959,0.0836135513055,0.0846557524026,0.0853813354448,0.0848536386868,0.0848932159437,0.08506471739,0.0854077202827,0.0855792217291,0.0865026910556,0.0875448921526,0.0872942361926,0.0874789300579,0.0876372390853,0.0881385510054,0.0886794401823,0.0890488279129,0.0896292943467,0.0900382593342,0.0894709853193,0.0891939445214,0.0898535654689,0.0897480261173,0.0905263788353,0.0911728073639,0.0913838860671,0.0922282008799,0.0929273990843,0.0934946730991,0.0947611453183,0.0965025446197,0.0977690168389,0.0984945998812,0.0988771800307,0.100104074993,0.101805897038,0.102016975741,0.102768943621,0.104629074693,0.10567127579,0.1059219317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m <- 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ycorr <- 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altd  <- c(231)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('Sarcophilus_harrisii-male-liver-H3K4me3-ERR572134.50mers.unique.MACS2_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) : 231',bty='n')
dev.off()