# R script for Peak Model
#  -- generated by MACS
p <- c(0.0496173211984,0.0578239231128,0.0661335367668,0.0745069195929,0.0821886521679,0.0825025927074,0.0821739362051,0.0824976873864,0.0824780661027,0.0821984628098,0.0821788415261,0.0820856404284,0.0822965692284,0.0820856404284,0.082944071591,0.0833904557956,0.0834100770793,0.0832285802049,0.0830470833305,0.082806722605,0.0827037108655,0.0827282374701,0.0824486341772,0.0827871013213,0.0823358117958,0.0817962264936,0.0817177413587,0.0813939901774,0.0815951083355,0.0815509604471,0.0816049189773,0.0811389134891,0.0806974346054,0.0802902929683,0.0802902929683,0.0800401216009,0.0799959737126,0.0801578493032,0.0800597428847,0.0798144768382,0.0793043234616,0.0796820331731,0.0801284173777,0.0800499322428,0.079829192801,0.0798929619731,0.0796575065685,0.0795937373964,0.0795348735452,0.0796624118894,0.0801382280195,0.0802167131544,0.0797801395917,0.0795348735452,0.0797163704196,0.0796329799638,0.0789118977872,0.0789707616384,0.0787058743082,0.0789658563175,0.0788530339361,0.0781270464386,0.0782840167083,0.0781466677223,0.0779504548851,0.0780142240572,0.0790541520942,0.0790541520942,0.0791179212663,0.0789805722802,0.0789217084291,0.079412240522,0.079000193564,0.0791277319081,0.0791669744756,0.0789168031082,0.078445892299,0.0782447741409,0.0781025198339,0.0779896974526,0.0774452068294,0.0771901301411,0.0774010589411,0.0773716270155,0.0771656035365,0.0770282545504,0.0766701661226,0.0765279118157,0.076572059704,0.0761502021041,0.0765818703459,0.0763709415459,0.0766211129133,0.0764150894343,0.0762679298064,0.0763758468669,0.0769693906993,0.0766358288761,0.0763611309041,0.0764052787924,0.0763562255832,0.0768124204296,0.0764298053971,0.0765328171366,0.0764935745692,0.0764837639273,0.0758902200949,0.0759785158716,0.0760520956855,0.0757087232205,0.0754879837787,0.0750955581044,0.0751740432392,0.0745118249138,0.0746786058254,0.0745020142719,0.0743940972115,0.0742420322627,0.0736975416396,0.0738643225511,0.0738250799837,0.0739771449325,0.0738054587,0.0742027896953,0.0740507247465,0.0738397959465,0.0734915181605,0.0735896245791,0.073530760728,0.0736975416396,0.0735454766907,0.0731187137699,0.072976459463,0.0731628616583,0.0730009860676,0.0727213827747,0.0732953053234,0.0728685424025,0.0727900572677,0.0727213827747,0.0727802466258,0.073040228635,0.073045133956,0.0726478029607,0.0725546018631,0.0727115721328,0.072073880412,0.0723829156305,0.0725300752584,0.0726232763561,0.0720395431655,0.0717599398725,0.0715097685052,0.0714999578633,0.0714999578633,0.0716324015284,0.0719806793143,0.0715833483191,0.0717746558353,0.0712939343843,0.0717157919842,0.07158825364,0.0712939343843,0.0711124375099,0.0710143310913,0.0710977215471,0.0711418694355,0.0714852419005,0.0714116620866,0.0713773248401,0.0713577035563,0.0711467747564,0.0712154492494,0.0714459993331,0.0713527982354,0.0709260353146,0.0707935916495,0.0706317160588,0.0707003905518,0.0706709586263,0.0704453138635,0.0707102011937,0.0706611479844,0.0706562426635,0.0704649351472,0.0712988397052,0.0710830055843,0.0709701832029,0.0705924734914,0.0708475501797,0.0713037450261,0.0714754312586,0.0717108866632,0.0715244844679,0.0717354132679,0.0709113193518,0.0708132129332,0.0707739703658,0.071033952375,0.0704943670728,0.0701068467194,0.0698076221427,0.0695231135288,0.0691797410638,0.0692238889522,0.0690571080406,0.0697536636125,0.0700577935101,0.0698419593892,0.0703717340496,0.070067604152,0.069861580673,0.0701264680031,0.0707396331193,0.0707298224774,0.0709505619192,0.0706611479844,0.0706120947751,0.0710633843006,0.0709799938448,0.0714214727284,0.0716667387749,0.0716471174912,0.0712743131006,0.0709996151285,0.0711320587936,0.0714361886912,0.0711909226448,0.0709358459564,0.0707347277983,0.0707102011937,0.0708083076123,0.070548325603,0.0703913553333,0.0703472074449,0.0703962606542,0.0696800837986,0.0699449711288,0.0700136456218,0.070067604152,0.0700038349799,0.0699155392032,0.0701951424961,0.0705679468868,0.0708083076123,0.0706709586263,0.0708181182541,0.0706758639472,0.0705777575286,0.070553230924,0.070273627631,0.0701706158915,0.0699694977334,0.070553230924,0.0704011659752,0.0705090830356,0.0708181182541,0.0706660533053,0.0708377395379,0.0710192364122,0.0711467747564,0.0713969461238,0.0715784429982,0.0709701832029,0.0709898044867,0.0709750885239,0.0708867927471,0.0709505619192,0.0706562426635,0.0709211299937,0.0709603725611,0.0712939343843,0.0714754312586,0.0720885963748,0.0720935016957,0.0722210400399,0.0727213827747,0.0728979743281,0.0732658733978,0.0728979743281,0.0731971989048,0.0730304179932,0.0727998679095,0.0724417794817,0.0725791284677,0.0726036550724,0.0719855846353,0.0718335196865,0.071867856933,0.0721523655469,0.0720248272027,0.0715833483191,0.0717697505144,0.0720248272027,0.0721278389422,0.0719855846353,0.0722161347189,0.0726625189235,0.0727802466258,0.07269685617,0.0729225009327,0.0733836011001,0.0737416895279,0.0738250799837,0.0744676770254,0.0755076050624,0.0757479657879,0.0761894446716,0.0766799767645,0.0766014916296,0.0770822130807,0.0773471004108,0.0778376325038,0.0781417624014,0.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m <- 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ycorr <- 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altd  <- c(2, 254)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('Rattus_norvegicus-male-liver-H3K4me3-ERR572172.50mers.unique.MACS2_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) : 2,254',bty='n')
dev.off()