# R script for Peak Model
#  -- generated by MACS
p <- c(0.0376257148083,0.0439571143533,0.0501434409136,0.0562054192013,0.0618425408912,0.0620083385879,0.0617492796867,0.0617907291109,0.0617492796867,0.0614902207855,0.0615420325658,0.0617389173307,0.061801091467,0.0622984845572,0.062692254087,0.0623813834056,0.0617700043988,0.0621637739286,0.0616145690581,0.0624124704738,0.0628891388519,0.0628684141398,0.0630238494806,0.0628166023596,0.0632518213136,0.0634797931466,0.0636352284874,0.0637595767599,0.0636455908434,0.063117110685,0.0634383437225,0.063334720162,0.0627855152915,0.0623088469133,0.0620083385879,0.0625057316782,0.0629409506322,0.0628684141398,0.0629409506322,0.0628684141398,0.0625264563903,0.0626093552387,0.0625989928826,0.0633554448741,0.0636974026236,0.0631067483289,0.0627026164431,0.0625575434584,0.0628373270717,0.0628269647157,0.0627233411552,0.0626611670189,0.0638113885402,0.0640186356611,0.0638735626765,0.0643502310546,0.0643916804788,0.0645367534635,0.0646196523119,0.0654279160836,0.0655833514243,0.0657905985452,0.0651170454021,0.0645782028877,0.0650030594856,0.065303567811,0.0652206689626,0.0655522643561,0.0653657419473,0.065085958334,0.064857986501,0.064433129903,0.0653553795912,0.065531539644,0.0651170454021,0.065085958334,0.065085958334,0.064868348857,0.0648787112131,0.0646921888042,0.0645160287514,0.0651481324703,0.0649097982812,0.0648994359251,0.064640377024,0.0640911721534,0.0642466074942,0.0643087816304,0.0648890735691,0.0649616100614,0.0651999442505,0.0652828430989,0.0645782028877,0.0646300146679,0.0648061747207,0.0651274077582,0.06465073938,0.0641429839337,0.0642984192744,0.0641533462897,0.0640808097974,0.0640393603732,0.0643087816304,0.0644849416833,0.0647543629405,0.0651170454021,0.0655626267122,0.0661118315827,0.0655937137803,0.0658216856134,0.0660807445146,0.0658631350376,0.066401977552,0.0662361798553,0.0670133565588,0.0669719071346,0.0676040108535,0.0669200953544,0.0675003872931,0.0671791542556,0.067054805983,0.0671687918995,0.0669408200665,0.0668786459302,0.0660911068706,0.0656869749848,0.0656040761364,0.0656662502727,0.0656662502727,0.0656558879166,0.0661532810069,0.0661221939387,0.0658942221057,0.0664641516883,0.0666299493851,0.0671998789677,0.0677594461942,0.0679874180273,0.0674589378689,0.0676350979217,0.0673864013765,0.0672516907479,0.0674071260886,0.0672206036798,0.0671791542556,0.0671169801193,0.0672102413237,0.0674693002249,0.0671791542556,0.0670133565588,0.0673864013765,0.0674382131568,0.0678008956184,0.0675418367172,0.067479662581,0.0675521990733,0.0672413283919,0.0674382131568,0.0690029289199,0.0690340159881,0.0682361145724,0.0685366228978,0.0680081427394,0.068142853368,0.0684640864055,0.0683397381329,0.0683397381329,0.0675107496491,0.0671584295435,0.0673345895963,0.0672931401721,0.067262053104,0.0671377048314,0.0671066177633,0.0669304577104,0.0670340812709,0.067044443627,0.0680081427394,0.0678837944668,0.0678008956184,0.0684226369813,0.0685366228978,0.0689303924276,0.0692101760409,0.0690029289199,0.069230900753,0.0689200300716,0.0686609711704,0.0684433616934,0.0695106843663,0.0701220633731,0.0700702515928,0.0699459033203,0.0708059788722,0.0714898943713,0.0712515601822,0.0715624308637,0.0716764167802,0.0718318521209,0.0712619225383,0.0706298188194,0.0703811222742,0.0708163412282,0.0700288021686,0.0697593809114,0.0702256869335,0.0699044538961,0.0704536587666,0.0703500352061,0.0704743834787,0.0711272119097,0.0714898943713,0.0714691696592,0.0720080121737,0.0719043886132,0.071417357879,0.0720598239539,0.0723188828551,0.0722256216507,0.0721116357342,0.0717075038483,0.0720183745297,0.0724743181958,0.0731996831192,0.0739457727546,0.0743395422844,0.0749509212912,0.07469186239,0.0756244744343,0.075790272131,0.0762980275773,0.0768990442281,0.0768057830237,0.0759664321838,0.0762876652213,0.0767643335995,0.0765052746983,0.0765881735467,0.0769612183644,0.0773653502502,0.077106291349,0.0769301312962,0.0775622350151,0.0781632516659,0.0777176703558,0.0779352798328,0.077966366901,0.0778109315603,0.0772617266898,0.0775933220833,0.078401585855,0.0783601364308,0.0782668752264,0.0776762209316,0.0785155717715,0.0783497740747,0.0779352798328,0.0785155717715,0.0785777459078,0.0790440519299,0.0787642683166,0.0785259341275,0.0791269507783,0.0798419533456,0.080152824027,0.0802978970117,0.0807227536096,0.0814066691087,0.0822667446607,0.0823600058651,0.0823807305772,0.0827952248191,0.081904062199,0.0820802222518,0.0816553656539,0.0821838458123,0.0830231966521,0.0827330506828,0.0824636294256,0.0828470365993,0.0830335590082,0.0831993567049,0.0835931262347,0.0828470365993,0.0831579072807,0.0824325423574,0.0825361659179,0.0829817472279,0.0833444296896,0.0826087024102,0.0830853707884,0.0832926179094,0.084080156969,0.084743347756,0.0847951595362,0.0857795833608,0.0854583503233,0.0856345103761,0.0852925526265,0.0862873388071,0.087582633313,0.0888261160387,0.0901732223249,0.0915928651034,0.0938207716536,0.0954787486212,0.0973439727097,0.099167747374,0.101312755076,0.102535513089,0.103437038066,0.10476341964,0.104307475974,0.105499146919,0.105405885715,0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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('Callithrix_jacchus-male-liver-H3K4me3-ERR572280.50mers.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) : 228',bty='n')
dev.off()