# R script for Peak Model
#  -- generated by MACS
p <- c(0.02084637988,0.0239087187034,0.0271677214879,0.0303986294208,0.0340931024049,0.0335031105215,0.0335312053731,0.0335593002247,0.0332783517088,0.0337840590374,0.0339526281469,0.0343319086434,0.0343319086434,0.0347252365657,0.0344021457724,0.0346971417141,0.0349921376558,0.0352449913201,0.0353573707265,0.0350904696363,0.0352309438943,0.0358209357777,0.0361580739968,0.0365935441964,0.0367902081576,0.0365794967706,0.036073789442,0.0357085563713,0.0352730861717,0.0347252365657,0.0348797582494,0.0337840590374,0.0334469208183,0.0332923991346,0.0330254980445,0.0329271660639,0.0332362094314,0.0332502568572,0.0337138219084,0.0343038137918,0.0337138219084,0.0341633395339,0.034430240624,0.0339807229985,0.034289766366,0.0344864303272,0.034430240624,0.0348516633978,0.0346830942883,0.0350342799332,0.0356804615197,0.0356945089455,0.0361861688484,0.0363547379579,0.0367761607318,0.0371132989509,0.0373661526152,0.0373661526152,0.0375487691505,0.0369025875639,0.0369025875639,0.036762113306,0.0367059236028,0.0365794967706,0.0366075916222,0.0365092596417,0.0366075916222,0.0363547379579,0.0362423585516,0.0368744927123,0.0362142637,0.0366075916222,0.0366637813254,0.036551401919,0.0369306824155,0.0373240103378,0.037309962912,0.0375347217247,0.0376190062795,0.0375628165763,0.0381809033113,0.0383916146982,0.0383635198466,0.0390518437106,0.038546136382,0.0382932827176,0.0386023260851,0.0386304209367,0.0386585157883,0.0383775672724,0.0383073301434,0.0380123342017,0.0376330537053,0.0372959154862,0.0372537732088,0.037239725783,0.0372959154862,0.037169488654,0.0374504371699,0.0376190062795,0.0378859073696,0.038405662124,0.0387287529173,0.0389956540074,0.0392766025233,0.0394451716329,0.0393749345039,0.0399368315357,0.0402177800516,0.0404144440127,0.0400913532194,0.040259922329,0.0402037326258,0.0400070686647,0.0397682624261,0.0402177800516,0.0406111079739,0.0404846811417,0.0403582543095,0.0407796770834,0.0410465781735,0.0406111079739,0.0410746730251,0.0416646649085,0.0421984670887,0.0417629968891,0.0414820483732,0.0414820483732,0.0415944277795,0.0410887204509,0.0410465781735,0.041355621541,0.0411589575799,0.0410606255993,0.0409763410445,0.0416084752053,0.0416225226311,0.0414680009474,0.0416646649085,0.0422546567919,0.042451320753,0.0427744115463,0.0424653681788,0.042521557882,0.0427041744173,0.0426620321399,0.0429570280816,0.0433924982813,0.0426760795657,0.0426479847142,0.0427884589721,0.0429008383785,0.0434346405587,0.0431958343202,0.0428586961011,0.0425777475852,0.0423248939209,0.0421141825339,0.0430413126364,0.0431115497654,0.043139644617,0.043069407488,0.0429429806559,0.0439403478873,0.0442212964032,0.0449096202672,0.0452327110605,0.0452608059121,0.0452186636347,0.0454996121506,0.0463986474015,0.0466515010658,0.0468341176011,0.0463565051241,0.0461317463114,0.0461879360145,0.0462300782919,0.0469745918591,0.047185303246,0.0468481650269,0.0462581731435,0.0463845999757,0.0464126948273,0.0469464970075,0.0474943466135,0.0477752951294,0.0481826704775,0.0480281487937,0.0483652870128,0.0489833737478,0.0494188439474,0.0492081325605,0.049517175928,0.0490536108768,0.0486743303803,0.0483652870128,0.0489131366188,0.0498824089987,0.0497840770181,0.0494328913732,0.0494609862248,0.0501071678114,0.0501493100888,0.0504443060305,0.0513152464298,0.0512028670234,0.0509640607849,0.0507954916754,0.0511326298944,0.0515961949457,0.0519473805906,0.0524249930676,0.0527340364351,0.0532116489121,0.053492597428,0.0539561624793,0.0540544944598,0.0537173562408,0.0537735459439,0.0538718779245,0.0538297356471,0.0532537911895,0.0538718779245,0.0543213955499,0.0545742492143,0.0550518616913,0.0551501936719,0.0554030473362,0.0556699484263,0.0559930392196,0.0564566042708,0.0571168332832,0.0569482641736,0.0569623115994,0.0568780270447,0.0570465961542,0.0575523034828,0.0577349200182,0.0577630148698,0.0581984850694,0.058774429527,0.0586339552691,0.0593082317072,0.0596594173521,0.0597858441843,0.0601651246807,0.0602915515129,0.0609236856737,0.0614012981507,0.0618227209246,0.0619912900341,0.0623284282532,0.0621317642921,0.0622300962726,0.0632836532073,0.0632696057815,0.0635926965748,0.0640843564776,0.0637472182585,0.0637893605359,0.0633257954847,0.0638174553875,0.0650536288575,0.0654750516313,0.0654469567797,0.0659245692568,0.0663319446048,0.0662195651985,0.0675119283716,0.0688745286737,0.0695909473893,0.0704478403628,0.0701668918469,0.0700545124405,0.0699842753116,0.0705602197692,0.0706585517497,0.071529492149,0.0719790097745,0.0712766384847,0.0720632943293,0.0719368674971,0.0726251913611,0.0732011358187,0.0740299339406,0.0743108824565,0.0752942022621,0.0757296724618,0.0758982415713,0.0765725180095,0.076333711771,0.0778227389053,0.0785532050466,0.0793960505943,0.0805479395095,0.0815734015926,0.0822195831792,0.0823179151597,0.0827955276368,0.0826550533788,0.0842143176421,0.0838631319972,0.0839614639778,0.084565503287,0.085113352893,0.0858297716085,0.0858297716085,0.0865040480467,0.0870659450785,0.0884144979548,0.0885971144902,0.0894680548895,0.0903530427146,0.0905637541015,0.09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m <- 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ycorr <- 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altd  <- c(221)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('A549-100nM-Dex-12h-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) : 221',bty='n')
dev.off()