# R script for Peak Model
#  -- generated by MACS
p <- c(0.0242175293746,0.0284306719351,0.0326438144957,0.0373393779601,0.0415364398238,0.0416972467917,0.0413756328558,0.0410218575263,0.041439955643,0.0420027800309,0.042388716754,0.0421635869988,0.0422600711796,0.041439955643,0.0416490047014,0.0418580537597,0.0419706186373,0.0424208781476,0.0420188607277,0.0419062958501,0.0421153449084,0.0422439904828,0.0422439904828,0.0428228955675,0.0428228955675,0.0426781692963,0.0427264113867,0.0427746534771,0.0430801867162,0.0425656044187,0.0424208781476,0.0424530395411,0.0421635869988,0.0424208781476,0.0427103306899,0.0426299272059,0.0429676218386,0.0431605902002,0.0435626076201,0.0441575934015,0.0445756915182,0.0447043370926,0.0452671614804,0.0451706772997,0.0445596108214,0.0446239336086,0.0449455475445,0.0448973054541,0.044752579183,0.0450741931189,0.0446882563958,0.0448329826669,0.0444792073374,0.0446239336086,0.0450098703317,0.0455244526292,0.0454762105388,0.0449937896349,0.0448973054541,0.0448973054541,0.0453475649644,0.0454762105388,0.0462963260754,0.0466661821017,0.0468591504632,0.0474219748511,0.0475988625158,0.0487566726851,0.0495767882217,0.0498662407641,0.049946644248,0.0499305635512,0.0497858372801,0.0499144828544,0.0508310825718,0.050895405359,0.0512813420821,0.0514743104436,0.0517959243796,0.0520049734379,0.052390910161,0.0535648010271,0.0544331586541,0.0551246286163,0.0554301618554,0.0558000178817,0.0569417473542,0.0576814594069,0.0583246872787,0.0593377711768,0.0597397885967,0.0601739674102,0.0603669357718,0.0608171952821,0.0613317775795,0.0618785212706,0.0615408266379,0.0618624405738,0.0625699912328,0.0631167349239,0.064049415338,0.0645639976355,0.0650946606298,0.0656735657144,0.0663167935862,0.0668313758837,0.0674746037556,0.0678444597819,0.067908782569,0.0683107999889,0.0690022699512,0.0691952383127,0.0701922415141,0.0704977747532,0.0706907431147,0.0713500516834,0.0719932795552,0.0728294757886,0.073344058086,0.07342446157,0.073585268538,0.0739068824739,0.0739229631707,0.0739872859579,0.0743088998938,0.074292819197,0.074292819197,0.0737299948092,0.0733923001764,0.0741641736226,0.0740355280483,0.0745179489521,0.0743249805906,0.0739390438675,0.0736817527188,0.0740516087451,0.074373222681,0.0749682084624,0.075000369856,0.0740355280483,0.0739390438675,0.0734566229636,0.0736978334156,0.0741641736226,0.0736174299316,0.0730063634533,0.0722988127943,0.0722023286135,0.0718646339808,0.0716716656193,0.0718003111936,0.0719128760712,0.0714626165609,0.0707872272955,0.071221406109,0.070594258934,0.0702083222109,0.0692434804031,0.0688897050736,0.0685520104409,0.067989186053,0.067362038878,0.0666223268254,0.0665419233414,0.0651268220234,0.0650624992362,0.0648534501778,0.0643067064868,0.0640333346412,0.0639368504605,0.0631971384078,0.0628916051687,0.0628755244719,0.0624091842648,0.0631328156207,0.0628916051687,0.0626986368072,0.0623770228713,0.0622966193873,0.0624252649616,0.0625217491424,0.0623609421745,0.0620232475417,0.0621840545097,0.0612031320052,0.0606403076173,0.060270451591,0.0607528724949,0.0602382901974,0.059402093964,0.0590804800281,0.0585015749434,0.0586784626082,0.0581638803107,0.0585498170338,0.0583568486723,0.057986992646,0.0577779435876,0.0581960417043,0.0580352347364,0.0576653787101,0.0577618628908,0.0567005369023,0.0562985194824,0.0563146001792,0.0566522948119,0.0565558106311,0.0562181159984,0.0554944846426,0.0556713723074,0.0554140811586,0.0550763865259,0.0550120637387,0.054835176074,0.0544331586541,0.0543205937765,0.0549959830419,0.0552532741907,0.0555748881266,0.0554462425522,0.0561377125144,0.0563146001792,0.0567648596895,0.057118635019,0.0573759261677,0.0575688945293,0.0568613438703,0.056491487844,0.0566683755087,0.056491487844,0.0565236492375,0.0567326982959,0.0568452631735,0.0566522948119,0.0568452631735,0.0568774245671,0.0571668771094,0.0571507964126,0.0568291824767,0.0575528138325,0.0573920068645,0.0580352347364,0.0584694135499,0.0590643993313,0.0587427853954,0.0590804800281,0.0595468202352,0.0599327569583,0.0605759848301,0.0605438234365,0.0606885497077,0.0607528724949,0.0611066478244,0.0618946019674,0.0623287807809,0.0621518931161,0.0622162159033,0.0631328156207,0.0628272823815,0.0630524121367,0.0634865909502,0.0635830751309,0.0638564469765,0.0638886083701,0.064210222306,0.0646283204227,0.0660595024375,0.0662363901023,0.0674102809684,0.0685037683505,0.0690987541319,0.0698223854878,0.0699510310621,0.0701118380301,0.0714626165609,0.0726043460334,0.0727812336982,0.0738425596867,0.074453626165,0.0747109173137,0.0761903414189,0.0768818113811,0.0787150108159,0.0808215820961,0.0814004871808,0.0829442340732,0.0837804303066,0.0846487879336,0.086031727858,0.0875111519632,0.0891513830364,0.0902609511153,0.0916599717366,0.0919011821885,0.093042911661,0.0941042376495,0.0956319038452,0.0966610684401,0.0980440083645,0.0993143834114,0.0996842394377,0.101549600266,0.102514442074,0.104218995934,0.105634097252,0.106711503938,0.108190928043,0.109879401206,0.111198018344,0.112050295274,0.113610122863,0.11452672258,0.114784013729,0.115925743202,0.116826262222,0.117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m <- 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ycorr <- 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altd  <- c(156, 335, 540)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('L43-Tetrahymena_thermophila-H3K4me3.2x36mers.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) : 156,335,540',bty='n')
dev.off()