# R script for Peak Model
#  -- generated by MACS
p <- c(0.0246453242675,0.0289195460809,0.0332582844499,0.037806701625,0.0418551154935,0.0417905989378,0.0414357578816,0.0409357545752,0.0411454333811,0.0418551154935,0.0420486651605,0.0418551154935,0.0416454366876,0.0411293042422,0.0412422082146,0.0416131784097,0.0419035029103,0.0421776982719,0.0418389863546,0.0418389863546,0.0418067280768,0.0420647942994,0.0422422148275,0.0426454433005,0.0429035095232,0.042742218134,0.0426938307173,0.0430648009124,0.0433228671351,0.0427260889951,0.0429196386621,0.0424518936335,0.0424357644946,0.0425970558838,0.0430002843567,0.0428067346897,0.0430970591902,0.0433067379962,0.0438067413026,0.0445809399707,0.0446454565264,0.0452099763886,0.0454519134723,0.0455809465837,0.0448873936102,0.0450970724161,0.0452099763886,0.0449680393048,0.0447744896378,0.0447583604988,0.0444196485815,0.0446777148042,0.0447099730821,0.044726102221,0.045113201555,0.0453390094999,0.0457906253896,0.0454035260556,0.0454357843334,0.0454035260556,0.0461938538626,0.0460164333345,0.0465809531966,0.0467261154469,0.047097085642,0.0478551551712,0.0479035425879,0.0490648405901,0.0497422644247,0.0502261385922,0.05025839687,0.0501777511755,0.0500003306473,0.050274526009,0.0510809829549,0.0510003372603,0.0512745326219,0.0512422743441,0.0515809862614,0.0519519564565,0.0522745392349,0.0535003537927,0.0543068107386,0.0548068140451,0.0548068140451,0.055403592185,0.0565326319093,0.0572584431607,0.0580165126898,0.0587907113579,0.059371360359,0.0596455557206,0.0600649133325,0.0608229828617,0.0615649232519,0.0620326682805,0.0617262146411,0.0620810556973,0.0626778338373,0.0632907411162,0.0640810689232,0.0649681715637,0.0652746252032,0.0659359198988,0.0665326980388,0.0671294761788,0.0680004496804,0.068468194709,0.0686133569593,0.0689520688766,0.0695811052944,0.0697101384058,0.0708230489911,0.0709520821025,0.0710004695192,0.0713553105754,0.0717585390484,0.0724843502997,0.0728553204949,0.073016611884,0.0730972575786,0.0733230655235,0.0734682277738,0.0736779065797,0.0742262973029,0.0744359761089,0.0743230721364,0.0738714562467,0.074016618497,0.0745166218035,0.0744359761089,0.0750327542489,0.0748392045818,0.0745972674981,0.074403717831,0.0749037211375,0.0752263039159,0.0758069529169,0.075597274111,0.075194045638,0.0755004992775,0.0752424330548,0.0749037211375,0.0751295290824,0.0747424297483,0.0738714562467,0.0733391946624,0.0734843569127,0.073016611884,0.0726778999668,0.0722585423549,0.0719037012987,0.0716940224927,0.0711133734917,0.071242406603,0.0710327277971,0.0703230456847,0.0693391682106,0.0692262642382,0.0685488404036,0.0682423867642,0.0677746417355,0.0674359298182,0.0671939927345,0.0658391450653,0.0655488205648,0.0657584993707,0.0653230126199,0.0652423669253,0.0652262377864,0.0641778437567,0.0639520358118,0.0636778404502,0.0633552576719,0.0639036483951,0.0636778404502,0.0635004199221,0.0632100954216,0.062742350393,0.0627907378097,0.0631455788659,0.0628713835043,0.0624520258924,0.0628713835043,0.061935893447,0.0611939530568,0.0605004000833,0.0606294331946,0.0599842676379,0.0592907146644,0.0592261981087,0.0585649034131,0.0587423239412,0.0577745756061,0.0580810292455,0.0581455458012,0.0580649001066,0.0578552213007,0.0583552246071,0.0581939332179,0.0574036054109,0.0576455424947,0.0568390855488,0.0566939232985,0.0567745689931,0.0569519895212,0.0565326319093,0.0560326286029,0.0554519796018,0.0555971418521,0.0555648835742,0.0553713339072,0.0551293968234,0.0548068140451,0.0545487478224,0.0544681021278,0.0550648802678,0.0556939166856,0.0560326286029,0.0557584332413,0.0566616650207,0.0569519895212,0.0571777974661,0.0579358669952,0.0583068371904,0.0585487742742,0.0583229663293,0.0576939299115,0.0576939299115,0.0576616716336,0.0575326385223,0.0574197345499,0.0578552213007,0.0574681219666,0.0573713471331,0.0572423140218,0.0573713471331,0.0575648968001,0.0572584431607,0.0580003835509,0.0578874795785,0.0586616782466,0.0589520027471,0.0591939398309,0.0590971649974,0.0596616848595,0.0597907179709,0.0598874928044,0.0607423371671,0.0608713702784,0.0608229828617,0.0605326583611,0.0604842709444,0.0614197610016,0.0617262146411,0.0612100821957,0.0615649232519,0.0624681550313,0.0620971848362,0.0622584762254,0.0626939629762,0.0630810623103,0.063726227867,0.0639681649508,0.0644681682572,0.0650649463972,0.0664843106221,0.0669520556507,0.0679843205415,0.0688875523209,0.0693714264885,0.0703230456847,0.0708875655468,0.0712585357419,0.0723230589106,0.0733230655235,0.0733714529403,0.0741456516083,0.0749037211375,0.075210174777,0.0766779264185,0.0771618005861,0.078371486005,0.0799198833412,0.0807102111482,0.0824682872903,0.0835973270146,0.0847747541556,0.0860489561302,0.0872263832712,0.0886941349128,0.0899199494706,0.0912909262787,0.091823187863,0.0926619030868,0.0936941679776,0.0946296580348,0.0954361149808,0.0966458003996,0.0982748434304,0.0990813003763,0.100694214268,0.101807124854,0.103420038745,0.105129727471,0.106403929445,0.108355555254,0.109791048618,0.111371704232,0.112178161178,0.113420104875,0.114436240627,0.114823339961,0.115613667768,0.116210445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m <- 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ycorr <- 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altd  <- c(155, 335, 539)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('L43-Tetrahymena_thermophila-H3K4me3.36mers.MACS-2.0.10_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) : 155,335,539',bty='n')
dev.off()