# R script for Peak Model
#  -- generated by MACS
p <- c(0.0281702941013,0.0330450923149,0.0379198905284,0.0426940291918,0.0480002254774,0.0479570856702,0.0477126267627,0.0478564261201,0.048129644899,0.0484891432923,0.0484891432923,0.0489493012358,0.0488486416857,0.0492512798862,0.0488630216214,0.0496539180867,0.0500565562872,0.050286635259,0.050444814552,0.0505310941664,0.0502578753875,0.0503585349376,0.0506892734595,0.0506461336523,0.0503729148734,0.0503729148734,0.0502578753875,0.0504304346163,0.0499846566086,0.0501140760302,0.0505886139094,0.0502434954518,0.0505742339736,0.0502434954518,0.0502003556446,0.0494813588579,0.049582018408,0.049208140079,0.0493231795648,0.049366319372,0.0492225200147,0.0491074805288,0.0485322830995,0.0488342617499,0.0490212009144,0.049582018408,0.049855237187,0.0501715957731,0.0507036533952,0.0510775317243,0.0514226501819,0.0515089297963,0.0519259479326,0.0518971880611,0.0522135466472,0.0523285861331,0.0520266074827,0.0518396683182,0.0517246288323,0.0513795103747,0.0507467932024,0.0508043129454,0.0501140760302,0.0502147355803,0.0501572158374,0.0492512798862,0.0493087996291,0.0497833375083,0.0492944196934,0.0493375595006,0.0495676384723,0.0496251582152,0.0501284559659,0.0498696171227,0.050286635259,0.0509481123027,0.050933732367,0.0509481123027,0.0510343919171,0.0510775317243,0.051149431403,0.050502334295,0.0504879543592,0.0503441550019,0.05001341648,0.0499127569299,0.0497401977011,0.0495676384723,0.0499990365443,0.049855237187,0.0499702766728,0.0507611731382,0.0509049724955,0.0513219906318,0.0513938903104,0.0516527291536,0.0522135466472,0.0523429660688,0.0522135466472,0.0522566864544,0.0520409874184,0.0518684281896,0.0515520696035,0.0516383492179,0.0519690877398,0.0518971880611,0.051796528511,0.0512644708888,0.0506892734595,0.0512788508246,0.0518396683182,0.0522710663902,0.0527312243336,0.0527599842051,0.0527312243336,0.0526449447192,0.0528606437552,0.0533064217629,0.0539247589995,0.0537234398992,0.0532920418272,0.0531482424699,0.0531913822771,0.0532632819557,0.0533783214416,0.0535796405419,0.0533927013773,0.0537521997707,0.0542267376499,0.0542267376499,0.0547156554648,0.0547444153363,0.0547012755291,0.0543849169429,0.0536515402205,0.0538528593208,0.0540973182283,0.0537809596421,0.0532057622128,0.0537234398992,0.0538384793851,0.0536227803491,0.0535652606061,0.0538097195136,0.0542123577141,0.0539535188709,0.0537234398992,0.0543849169429,0.054974494308,0.0548450748864,0.0548738347579,0.0552045732797,0.0557510108376,0.0558660503234,0.0564124878813,0.0565562872386,0.0569733053749,0.0567144665317,0.0571602445394,0.057289663961,0.056858265889,0.056700086596,0.0567719862746,0.056858265889,0.0568007461461,0.0570308251178,0.0567719862746,0.057778581776,0.0571890044109,0.0570452050536,0.0578073416474,0.0578361015189,0.0579799008762,0.0588283170845,0.0588283170845,0.0583250193338,0.0589433565704,0.0581668400408,0.058152460105,0.0579799008762,0.0575916426114,0.0580086607477,0.0573184238325,0.0569589254392,0.057347183704,0.0583393992696,0.0578648613904,0.0578073416474,0.058152460105,0.0584688186912,0.0586988976629,0.0586557578557,0.0590296361847,0.059446654321,0.0596335934855,0.0595616938069,0.0601800310434,0.0600218517503,0.0599787119431,0.0594610342567,0.0590871559277,0.0591159157991,0.0597917727786,0.0587707973416,0.0583106393981,0.0578217215832,0.057505362997,0.0572752840253,0.0576491623544,0.0581237002336,0.0583106393981,0.0586557578557,0.058425678884,0.0585119584984,0.0586557578557,0.0592453352207,0.0592884750279,0.0596335934855,0.0593603747066,0.0596911132285,0.0594178944495,0.0590296361847,0.0595185539997,0.0599643320074,0.059878052393,0.0598061527143,0.0598924323287,0.0599355721359,0.0599643320074,0.0594610342567,0.0602375507863,0.0608558880229,0.0605107695653,0.0608271281514,0.0602231708506,0.0601512711719,0.0601656511077,0.0602663106578,0.0602087909149,0.0608846478943,0.060740848537,0.0607120886655,0.0601081313647,0.060309450465,0.0610140673159,0.0610715870589,0.0612729061591,0.0617330641026,0.0616180246167,0.0612872860949,0.0617186841669,0.0614167055165,0.0625095806322,0.062250741789,0.0621932220461,0.0623945411463,0.0625958602466,0.062035042753,0.0623082615319,0.0623082615319,0.0623945411463,0.0623945411463,0.0616324045525,0.0616755443597,0.062035042753,0.0622651217247,0.0623514013391,0.0623082615319,0.0630703981258,0.0631998175474,0.0628690790255,0.062840319154,0.0628115592826,0.0633579968404,0.0631998175474,0.0630703981258,0.0629409787042,0.0638037748482,0.0634730363263,0.0638181547839,0.0642495528559,0.0646378111207,0.0647672305423,0.0648247502852,0.0655149872004,0.0658744855937,0.06629150373,0.0658744855937,0.0659176254009,0.0665791024447,0.0665934823804,0.0672980992313,0.0676432176889,0.0675713180103,0.0674275186529,0.0675569380745,0.0681465154396,0.0684628740257,0.0688942720977,0.0687504727404,0.069253770491,0.0697139284345,0.0708787032289,0.0721297576377,0.0729637939102,0.0737403104398,0.0745743467123,0.0755378024065,0.0770908354656,0.0787157682035,0.0794779047973,0.0802831811984,0.081275396764,0.0813760563141,0.08192249387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m <- 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ycorr <- 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altd  <- c(150)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('GSE29282-OCI-LY1_BCL6_N-3_rep2_CHIP-GSM763402.36mers.unique.dedup.pseudoRep2.dedup.pseudoRep2.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) : 150',bty='n')
dev.off()