# R script for Peak Model
#  -- generated by MACS
p <- c(0.0365462195007,0.0428567306817,0.0489600972988,0.0548489213317,0.06101887013,0.0614701493586,0.0615293335198,0.0612704028148,0.0613073929155,0.0614405572781,0.0611298404321,0.0608857057674,0.0610040740897,0.0613887711371,0.0615071394593,0.0616181097615,0.0618178563053,0.0623801058361,0.0629645494273,0.0631864900315,0.0638301177839,0.0641112425493,0.0644071633549,0.0641112425493,0.0638523118443,0.0633862365754,0.0636525653005,0.0632900623135,0.0625354642591,0.0619954087887,0.0612334127141,0.0610114721098,0.0604566205992,0.0606341730826,0.0606785612035,0.0608857057674,0.0606933572437,0.06101887013,0.0609226958681,0.0611816265731,0.0613221889558,0.0611816265731,0.061122442412,0.0615219354996,0.0614257612378,0.0615663236205,0.0614553533183,0.0611594325127,0.0617882642247,0.0617438761039,0.0615515275802,0.0615589256003,0.0617290800636,0.0613369849961,0.0615071394593,0.0612999948954,0.061122442412,0.0614109651975,0.0604640186193,0.0608709097271,0.0612851988551,0.0614331592579,0.0616846919427,0.0616329058017,0.0610780542911,0.0609374919084,0.0609078998278,0.0607451433847,0.0609892780494,0.0608561136869,0.0607007552639,0.0604936106999,0.0602198839547,0.0599313611691,0.060708153284,0.0608265216063,0.0611890245932,0.0612999948954,0.0616698959025,0.0617142840233,0.0619140305671,0.0620989810707,0.0624836781181,0.0625576583195,0.0628165890244,0.0634380227164,0.0627869969439,0.0629571514071,0.0629571514071,0.062742608823,0.0626538325813,0.0630089375481,0.0627352108029,0.0629867434877,0.0627204147626,0.0625872504,0.062794394964,0.0628017929842,0.0629719474474,0.0628905692259,0.0631716939913,0.0633418484545,0.0635637890588,0.0633566444948,0.0634084306358,0.0629719474474,0.0630385296287,0.0625798523799,0.0624910761382,0.0627056187223,0.0629349573467,0.0624836781181,0.0625132701986,0.0628313850647,0.0624466880174,0.0622691355339,0.0625576583195,0.0628905692259,0.062639036541,0.0629423553669,0.0625946484202,0.0625502602993,0.0621211751311,0.0619288266074,0.0620693889901,0.0623949018764,0.0625872504,0.062639036541,0.0632900623135,0.0629719474474,0.0631421019107,0.0633862365754,0.0632900623135,0.0638523118443,0.0636895554012,0.0638819039249,0.0636673613408,0.063682157381,0.0631938880517,0.0632900623135,0.0629201613064,0.0624614840576,0.0632752662732,0.0632160821121,0.0637931276832,0.0635341969782,0.0638597098644,0.0638301177839,0.06414823265,0.0640150682874,0.0641408346298,0.064725278221,0.064828850503,0.0645995118786,0.0648214524829,0.0652283435907,0.0653615079532,0.0657018168798,0.0655982445978,0.0659829416452,0.066338046612,0.0664564149342,0.0662936584911,0.0670556545657,0.0667153456392,0.0665082010752,0.0666191713774,0.0665229971155,0.0669224902032,0.0671814209081,0.0673589733915,0.0674995357742,0.0672406050693,0.0668559080219,0.0670038684247,0.0672480030894,0.0671074407067,0.0669298882233,0.0669520822837,0.0666857535586,0.0663750367127,0.0665821812766,0.0670630525859,0.0672554011096,0.067432953593,0.0674255555728,0.0674625456735,0.0675217298347,0.0672554011096,0.0676622922174,0.0678916308418,0.0675439238951,0.067381167452,0.0674995357742,0.0678250486605,0.0678694367813,0.0679656110432,0.0686166368157,0.0693564388298,0.0694452150715,0.0697337378571,0.0701924151059,0.070199813126,0.0704291517504,0.0698669022196,0.0704365497706,0.0707398685964,0.0705179279921,0.0702811913476,0.0703625695691,0.0705475200727,0.0704809378914,0.0706215002741,0.0711245656437,0.0712207399056,0.0714426805098,0.0717164072551,0.0720197260809,0.0719753379601,0.072544985511,0.072648557793,0.0730332548403,0.0734623400086,0.0732182053439,0.0743501024256,0.0740171915192,0.0737360667538,0.0743944905464,0.0750381182988,0.0748975559161,0.0749715361175,0.0752822529635,0.0757187361518,0.0753562331649,0.0746756153118,0.0748013816542,0.075467203467,0.0745128588687,0.0742613261839,0.0742021420228,0.0747421974931,0.0741503558818,0.0739654053782,0.0746608192715,0.0756669500108,0.0759036866554,0.0761108312193,0.0764215480653,0.0765695084681,0.0767840510523,0.0766064985689,0.0772057382003,0.0778049778318,0.0781526847785,0.0779529382347,0.0787593224301,0.0786853422287,0.0791958056185,0.0795213185047,0.0799430056528,0.0800317818945,0.0798616274313,0.0799651997133,0.0798246373306,0.0800983640758,0.0799208115924,0.0807493898483,0.0814522017618,0.0820514413933,0.0824065463601,0.0830205820318,0.0837899761266,0.0835680355223,0.0839009464287,0.0844927880401,0.0844779919998,0.0845889623019,0.0846703405235,0.0849292712284,0.0847221266645,0.0847665147853,0.0852399880744,0.085950198008,0.0864606613978,0.086001984149,0.0866160198208,0.0863422930755,0.0864236712971,0.0863053029748,0.0862165267331,0.0867935723042,0.0867121940826,0.0862683128741,0.0860611683101,0.086312700995,0.0863940792165,0.0869859208279,0.0876739367011,0.088347156534,0.0891979288503,0.0897157902602,0.0908994734829,0.0919425943229,0.0933260240894,0.0944209310704,0.0957155845953,0.0968252876165,0.0979349906378,0.0990446936591,0.099976844197,0.100598277889,0.100339347184,0.101449050205,0.101441652185,0.1020556878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m <- 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ycorr <- 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altd  <- c(247)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('Sus_scrofa-male-liver-H3K4me3-ERR572197.50mers.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) : 247',bty='n')
dev.off()