# R script for Peak Model
#  -- generated by MACS
p <- c(0.0291965401906,0.0342674501395,0.0391184481774,0.0437495343042,0.0481865805095,0.0484064924205,0.0484323644101,0.0478890526298,0.048044284567,0.0484453004048,0.0484194284153,0.0481865805095,0.0482900684676,0.0485358523682,0.0483676844362,0.0481995165043,0.0482771324729,0.0480830925514,0.0483030044624,0.0482900684676,0.0484194284153,0.0483288764519,0.0483288764519,0.0486522763211,0.0494543079967,0.04927320407,0.0494025640177,0.0495319239653,0.04927320407,0.0491826521066,0.0488075082583,0.0491179721328,0.0488333802479,0.0489109962165,0.0490662281537,0.0493508200386,0.0495319239653,0.0497130278921,0.0497777078659,0.0496095399339,0.0499329398031,0.0496224759287,0.0503080836514,0.0503727636252,0.0506573555101,0.0507349714787,0.0507867154578,0.0510583713479,0.0511618593061,0.0513817712171,0.0515887471334,0.0519768269764,0.05149819517,0.0514464511909,0.0509031394107,0.0508902034159,0.0515111311648,0.0516275551177,0.0520415069503,0.0522355468718,0.0513558992276,0.0521320589136,0.0522743548561,0.0518086590444,0.0520026989659,0.0523390348299,0.0515628751438,0.0510454353531,0.0511618593061,0.0515499391491,0.0525201387567,0.0517957230497,0.0519509549869,0.0523649068194,0.0521579309032,0.0523260988351,0.0521449949084,0.0530246425526,0.0532574904584,0.0534903383642,0.0536585062962,0.0540724581288,0.0543053060346,0.0545898979195,0.0546028339142,0.0545252179456,0.0549650417677,0.0550167857468,0.0548744898044,0.0547063218724,0.0541888820817,0.0539042901968,0.0538654822125,0.0541371381026,0.0547192578672,0.0545122819509,0.0548486178148,0.0549909137573,0.0550555937311,0.0552108256683,0.0558317534172,0.0555859695166,0.0559999213492,0.0557153294643,0.0556506494904,0.0559999213492,0.0554954175532,0.0549262337834,0.0552755056422,0.055340185616,0.0550555937311,0.0554695455637,0.0554695455637,0.0557153294643,0.0554824815584,0.0551590816893,0.0552755056422,0.0554824815584,0.0554048655898,0.0553919295951,0.0556118415061,0.0554178015846,0.0555471615323,0.0553272496212,0.0555212895427,0.0567372730509,0.0573064568207,0.0572288408521,0.0572935208259,0.0569701209567,0.0570736089149,0.0576427926846,0.0573064568207,0.0574099447788,0.057513432737,0.057177096873,0.056957184962,0.0579920645434,0.0580955525015,0.0588199682085,0.058625928287,0.0585224403288,0.0588329042033,0.0590657521091,0.0596090638893,0.0593115360097,0.0598031038108,0.0588717121876,0.0595831918998,0.059570255905,0.0601523756696,0.0603981595702,0.0604757755388,0.061019087319,0.0609544073452,0.06123899923,0.0608121114027,0.0614201031568,0.0614718471359,0.0616658870574,0.0621833268481,0.0623385587853,0.062855998576,0.062467918733,0.0626102146754,0.0630500384975,0.0639296861417,0.0640590460894,0.0633605023719,0.0638779421626,0.0633734383667,0.063024166508,0.0622609428167,0.0627913186022,0.0624808547277,0.0620280949109,0.0621186468742,0.0626619586545,0.0629594865341,0.0624937907225,0.0624937907225,0.0630500384975,0.0635674782882,0.0640331740999,0.0656113654615,0.0658442133673,0.0658571493621,0.0657148534197,0.0662322932104,0.0667756049906,0.0675517646767,0.0674353407238,0.0681597564307,0.0684831562999,0.0672671727918,0.0674353407238,0.0668920289435,0.0666203730534,0.0661029332627,0.0659347653307,0.0660253172941,0.0669437729226,0.0669696449121,0.0662193572156,0.0669825809069,0.0678622285511,0.068534900279,0.0700872196511,0.0704235555151,0.0706693394157,0.0706175954366,0.0705529154628,0.0705270434732,0.0712773311697,0.0710315472692,0.0707081474,0.0705787874523,0.0699061157244,0.0706305314314,0.0703330035517,0.0713678831331,0.0712385231854,0.0715877950442,0.0716136670337,0.0717430269814,0.0720017468767,0.0724803786831,0.0726485466151,0.0729072665105,0.073269474364,0.0728813945209,0.0732047943901,0.0739680180814,0.0737222341808,0.0745889458303,0.0755332734483,0.0761283292076,0.0761800731867,0.0760377772442,0.0766198970088,0.0768527449146,0.0773960566948,0.0773572487105,0.0783015763286,0.0787414001507,0.0784050642867,0.0781592803861,0.0785473602292,0.0789095680827,0.0792459039466,0.079000120046,0.0799315116693,0.079892703685,0.0798409597059,0.0792588399414,0.0792200319571,0.0796210477949,0.0803842714862,0.0813156631094,0.0817813589211,0.0825057746281,0.0828162385025,0.083954606042,0.0842650699165,0.0843426858851,0.0855198614089,0.0860631731892,0.0867875888962,0.0865806129799,0.0860631731892,0.0873179646816,0.0874990686084,0.0860243652049,0.0861666611473,0.0877060445247,0.0877577885037,0.0871239247601,0.087240348713,0.0878224684776,0.0889737720119,0.0885856921689,0.0878742124566,0.0893747878497,0.0897887396823,0.089633507745,0.0903320514625,0.0917420748922,0.0917420748922,0.0913410590544,0.0909917871956,0.0908882992375,0.0915997789497,0.0917162029026,0.0931520983218,0.093423754212,0.092751082484,0.0928545704422,0.0935401781649,0.0950407535579,0.096204993087,0.097873736412,0.0994131197894,0.100874887198,0.102116742696,0.103177494267,0.105389549372,0.107304076598,0.10771802843,0.1082872122,0.109335027776,0.109723107619,0.110615691258,0.111120195054,0.110952027122,0.111741122803,0.11159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m <- 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ycorr <- 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altd  <- c(257)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('Macaca_mulatta-female-liver-H3K4me3-ERR572255.50mers.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) : 257',bty='n')
dev.off()