# R script for Peak Model
#  -- generated by MACS
p <- c(0.0217745948379,0.0257583559389,0.0291235205957,0.0330825378389,0.0369425796511,0.0371900182288,0.0370662989399,0.0368930919356,0.0371900182288,0.0373632252332,0.0373384813754,0.0367446287889,0.0373137375177,0.0368930919356,0.0370168112244,0.0375116883798,0.0372889936599,0.0368930919356,0.0366209095001,0.0363239832068,0.0363982147801,0.0360765446291,0.035556923616,0.0356064113315,0.0347403763095,0.0344929377318,0.0348640955984,0.0350867903183,0.0351610218916,0.0350867903183,0.0347156324518,0.0350620464606,0.035012558745,0.0349383271717,0.0355074359004,0.0349630710295,0.0346414008785,0.0347898640251,0.0348393517406,0.0354826920426,0.0357301306204,0.036200263918,0.0365466779268,0.0366209095001,0.0369425796511,0.037165274371,0.0370415550822,0.0367941165045,0.0369920673666,0.0367198849312,0.0368930919356,0.0368930919356,0.0366703972156,0.036521934069,0.0360765446291,0.0363982147801,0.0370415550822,0.0376848953842,0.0380560532508,0.0381302848241,0.0378333585308,0.037709639242,0.0380560532508,0.0386251619795,0.0389715759883,0.0389220882727,0.0392932461393,0.0385014426906,0.0384766988329,0.039219014566,0.0395901724325,0.0397138917214,0.0395901724325,0.0391447829927,0.0391200391349,0.038674649695,0.0379323339619,0.0389715759883,0.0386993935528,0.0376848953842,0.0378086146731,0.0378581023886,0.0381302848241,0.0383777234018,0.0384766988329,0.0386993935528,0.0394911970014,0.0386251619795,0.038674649695,0.0392437584237,0.0394664531437,0.0391942707082,0.0394664531437,0.0398376110102,0.0399118425835,0.0399613302991,0.0395654285748,0.0398870987258,0.039862354868,0.0402335127346,0.0400850495879,0.0400850495879,0.0396396601481,0.039862354868,0.0394911970014,0.0405304390278,0.0405551828856,0.0409510846099,0.0413469863342,0.0406294144589,0.0407778776055,0.0414212179075,0.0414459617653,0.0411985231876,0.0419160950629,0.0412727547609,0.0408521091788,0.0402582565923,0.0399118425835,0.0406294144589,0.0406789021744,0.0405304390278,0.0399613302991,0.0399860741568,0.0397633794369,0.0397138917214,0.0399118425835,0.0402087688768,0.0399365864413,0.0399365864413,0.039540684717,0.0395159408592,0.0398376110102,0.0397633794369,0.0393922215704,0.0393674777126,0.0395159408592,0.0396396601481,0.0396149162903,0.0387241374106,0.0388231128416,0.0389715759883,0.0393922215704,0.039540684717,0.0397138917214,0.0396149162903,0.0396149162903,0.0396396601481,0.0405799267433,0.0409015968943,0.0410748038987,0.0405304390278,0.0406294144589,0.0408768530366,0.0413469863342,0.0409510846099,0.041371730192,0.0410995477565,0.0407778776055,0.0412232670454,0.0412232670454,0.0422130213562,0.0420893020673,0.0417923757741,0.0418418634896,0.0419160950629,0.042015070494,0.0432275195248,0.0434749581025,0.0437223966802,0.0443162492667,0.0438956036846,0.0439945791156,0.04416778612,0.0442667615511,0.0446626632754,0.0445389439866,0.0438708598268,0.0440935545467,0.0443409931244,0.043846115969,0.043846115969,0.0446131755599,0.0442667615511,0.044489456271,0.0448606141376,0.0451327965731,0.045355491293,0.044489456271,0.0447616387065,0.0445389439866,0.0451575404308,0.04416778612,0.0444399685555,0.04416778612,0.0443657369822,0.0443162492667,0.0441430422623,0.0443162492667,0.0436481651069,0.0437471405379,0.0429553370893,0.0437223966802,0.0440440668312,0.0440193229734,0.0440193229734,0.0436976528224,0.044489456271,0.0450090772842,0.0452565158619,0.0460235754528,0.0464442210349,0.0466421718971,0.0463947333194,0.046543196466,0.0467906350437,0.0471370490525,0.0460235754528,0.0458256245906,0.0459246000217,0.0455534421552,0.0451822842886,0.0450090772842,0.0456524175863,0.0453060035775,0.0455534421552,0.0457019053018,0.0469390981903,0.0472360244836,0.0476071823501,0.0474339753457,0.0477556454967,0.0468401227592,0.0460978070261,0.0455781860129,0.0442420176933,0.0442667615511,0.0442172738356,0.0439203475423,0.0438213721112,0.0444152246977,0.0441182984045,0.0455286982974,0.0461720385994,0.0474339753457,0.0489680945275,0.0493145085363,0.049660922545,0.0504279821359,0.0507249084292,0.0506011891403,0.0506011891403,0.0503784944204,0.0505517014248,0.0510465785802,0.0502795189893,0.0506754207136,0.049561947114,0.0491907892474,0.0485227050876,0.0487453998075,0.0491907892474,0.0490918138163,0.0492650208207,0.0493145085363,0.0497598979761,0.0492650208207,0.0502795189893,0.0509476031491,0.051071322438,0.0510218347224,0.0510960662957,0.05149196802,0.0515909434511,0.0514672241623,0.0519373574599,0.0520858206065,0.0519868451755,0.0516156873089,0.0521600521798,0.0522095398954,0.0527539047663,0.0528281363396,0.053001343344,0.0529765994863,0.0531250626329,0.0540158415126,0.0537931467927,0.0543622555214,0.0540405853704,0.0548076449613,0.0554014975478,0.0551788028278,0.0553025221167,0.0548076449613,0.0548571326768,0.0550798273967,0.056341764143,0.0568613851562,0.0579006271826,0.0584697359113,0.060548219964,0.0627751671633,0.0644082617762,0.0672785492775,0.0700498613478,0.0719056506806,0.0744542680309,0.0766317275147,0.0796999658782,0.082199095513,0.0834362884015,0.0843270672813,0.0858859303208,0.086356063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m <- 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ycorr <- 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altd  <- c(52)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('RXRa_RA-GSM1603272.1x50mers.mm10.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) : 52',bty='n')
dev.off()