# R script for Peak Model
#  -- generated by MACS
p <- c(0.0409952622105,0.0478199156593,0.0546271274966,0.0614766975335,0.0681568347721,0.0684035089931,0.0684508505103,0.0683462008408,0.0681518514545,0.0680945433021,0.0679824186562,0.0679400604566,0.0679500270918,0.0679948769502,0.0680023519266,0.0678553440575,0.0677382360939,0.0678603273751,0.0678653106927,0.0676809279416,0.0677407277527,0.0677706276583,0.068009826903,0.0676435530596,0.0675712949544,0.0675364117313,0.0675189701197,0.0673495373214,0.0673445540038,0.0671825961819,0.0670355883128,0.0669807718192,0.0668088473621,0.0669608385488,0.0669483802548,0.0671551879351,0.0671028631003,0.0672100044287,0.0672997041454,0.0673844205446,0.0674541869909,0.0673744539094,0.067391895521,0.0674691369437,0.0674492036733,0.0671302713471,0.0671825961819,0.0669757885016,0.0669508719136,0.0668960554201,0.0667216393042,0.0665671564587,0.0666144979759,0.0663977236604,0.0664326068836,0.0667041976926,0.0667216393042,0.0667814391153,0.0667565225274,0.0668312722913,0.0669608385488,0.0671078464179,0.0669807718192,0.0670854214888,0.0671302713471,0.0668885804437,0.0666693144694,0.0665821064115,0.0663728070724,0.066340415508,0.0663453988256,0.0662855990145,0.0661884243213,0.0661111828986,0.0658769669715,0.0657498923728,0.0659392584415,0.0659816166411,0.0659716500059,0.0660214831818,0.0657922505724,0.0658694919951,0.0657424173964,0.0657797922784,0.065759859008,0.0658819502891,0.0660837746518,0.0660713163578,0.0660140082054,0.0658495587247,0.06579723389,0.0659492250767,0.0659292918063,0.0656801259264,0.0659591917119,0.0658171671604,0.0656253094329,0.0657872672548,0.0659616833707,0.0660339414758,0.0663379238492,0.0662382574973,0.0665073566475,0.066699214375,0.0665272899179,0.0664425735188,0.0663927403428,0.0662357658385,0.0659567000531,0.0661435744629,0.0660164998642,0.066031449817,0.0658969002419,0.0661884243213,0.0662058659329,0.0664749650831,0.0665970563643,0.0666443978814,0.066945888596,0.0666842644222,0.0667565225274,0.0664699817655,0.0662706490617,0.0660837746518,0.0663379238492,0.0662706490617,0.0662756323793,0.0661983909565,0.0659766333235,0.0661934076389,0.0659567000531,0.0661784576861,0.066352873802,0.0662855990145,0.0661261328514,0.0659292918063,0.0657424173964,0.0656577009973,0.0658171671604,0.065697567538,0.0657872672548,0.065822150478,0.0657673339844,0.0656801259264,0.0655156764457,0.0657199924672,0.0659791249823,0.0661336078278,0.0661958992977,0.0663728070724,0.0663827737076,0.0663703154136,0.0663379238492,0.0664301152248,0.0665322732355,0.0665272899179,0.0662880906733,0.0660862663106,0.066081282993,0.0658595253599,0.0660339414758,0.0659367667827,0.0659492250767,0.0660588580638,0.0662581907677,0.0665073566475,0.0666269562698,0.0668661555145,0.0667789474565,0.0669757885016,0.0668013723857,0.0668237973149,0.0669483802548,0.0668337639501,0.0666718061282,0.0664625067891,0.06644008186,0.0663977236604,0.0666568561754,0.0666294479286,0.0667316059394,0.0670879131476,0.0669782801604,0.0671227963707,0.067342062345,0.0672448876519,0.0675538533429,0.0675513616841,0.0675214617785,0.0675912282248,0.0678528523987,0.0677357444351,0.0678154775167,0.0677482027291,0.067700861212,0.0678952105982,0.0677282694587,0.067959993727,0.0679051772334,0.0680197935382,0.0679699603622,0.0679325854802,0.0680023519266,0.0683063343,0.0680646433965,0.068022285197,0.0680397268085,0.0679425521154,0.0680447101261,0.0680820850081,0.0682614844416,0.0682266012184,0.0680746100317,0.0677930525875,0.0680646433965,0.0682290928772,0.0682913843472,0.0683462008408,0.0684134756283,0.0685679584738,0.0684035089931,0.0685978583794,0.0688146326949,0.0693005061606,0.0693553226541,0.0696368800983,0.0698063128966,0.0700330538473,0.0702797280683,0.0700853786821,0.0700953453172,0.0698287378258,0.0699234208602,0.0699433541305,0.0701327201992,0.0700305621885,0.0700230872121,0.0702597947979,0.0700504954589,0.0705413522422,0.0711044671306,0.0714508077036,0.0718096065706,0.0718444897937,0.072051297474,0.0723502965298,0.0726268706564,0.0726841788088,0.0729507863002,0.0728486282895,0.0726169040213,0.0728909864891,0.0728710532187,0.0729383280062,0.0729233780535,0.0730355026994,0.0731874938861,0.0733394850728,0.0737306755041,0.0740221995836,0.0742813320986,0.0745803311544,0.0747672055643,0.0750238464205,0.0754324784635,0.0753801536287,0.0753776619699,0.0755296531566,0.0755221781802,0.0754175285107,0.0757115442489,0.0757788190365,0.0760479181867,0.0763768171481,0.0764241586652,0.0766284746867,0.0767455826502,0.0768876072018,0.0770470733649,0.0773286308091,0.0774856053134,0.0773610223735,0.0774806219958,0.0775005552662,0.0778269625688,0.0779540371675,0.0785520352791,0.078713993101,0.0787737929122,0.0790005338628,0.0791051835323,0.0796807567148,0.0796832483736,0.0796184652448,0.0794963739637,0.0797829147255,0.0796558401268,0.0798875643951,0.0804382209895,0.0810686106655,0.0817986666934,0.0823219150411,0.0832936619725,0.0844099251142,0.0855635631379,0.0866773346208,0.0878882807968,0.0889821190093,0.0896349336145,0.0899513742819,0.0903101731489,0.0906365804515,0.0911623204579,0.091538560936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m <- 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ycorr <- 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altd  <- c(225)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('C2C12-myocyte-H3K27ac-AM_39113_31814008-RT_Fix_5158-5933_IP_B3-17875.mm10.36mers.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) : 225',bty='n')
dev.off()