# R script for Peak Model
#  -- generated by MACS
p <- c(0.0305910490163,0.033585976892,0.0370087516071,0.0408593731616,0.0455656883949,0.0464213820736,0.0464213820736,0.0464213820736,0.0459935352343,0.046207458654,0.0459935352343,0.0500580802084,0.051769467566,0.0532669315039,0.0534808549236,0.051769467566,0.0521973144054,0.0524112378251,0.0541226251826,0.0556200891205,0.0554061657008,0.0556200891205,0.0558340125402,0.0554061657008,0.0562618593796,0.0551922422811,0.0543365486023,0.0536947783432,0.0513416207266,0.0496302333691,0.0492023865297,0.0474909991721,0.0498441567888,0.0485606162706,0.0479188460115,0.0481327694312,0.0492023865297,0.0504859270478,0.0521973144054,0.0556200891205,0.0558340125402,0.0560479359599,0.0528390846645,0.0556200891205,0.0558340125402,0.0571175530584,0.0569036296387,0.0584010935765,0.0554061657008,0.0539087017629,0.0543365486023,0.054550472022,0.0564757827993,0.0575453998977,0.0560479359599,0.0571175530584,0.0573314764781,0.0558340125402,0.0575453998977,0.0598985575144,0.0592567872553,0.0588289404159,0.0598985575144,0.059470710675,0.0613960214522,0.059470710675,0.0605403277735,0.0603264043538,0.0598985575144,0.0596846340947,0.059470710675,0.0635352556492,0.0616099448719,0.0613960214522,0.0648187961673,0.0675998006234,0.0665301835249,0.0669580303643,0.0667441069446,0.064390949328,0.0635352556492,0.0598985575144,0.0598985575144,0.0588289404159,0.0556200891205,0.0556200891205,0.0560479359599,0.0560479359599,0.0571175530584,0.0575453998977,0.059470710675,0.0620377917113,0.0616099448719,0.0639631024886,0.0607542511932,0.0609681746129,0.0611820980325,0.0620377917113,0.0616099448719,0.0607542511932,0.0626795619704,0.0596846340947,0.0590428638356,0.0560479359599,0.0590428638356,0.0573314764781,0.056689706219,0.0558340125402,0.0558340125402,0.0571175530584,0.0549783188614,0.0560479359599,0.0562618593796,0.0564757827993,0.0584010935765,0.0616099448719,0.0609681746129,0.0607542511932,0.0620377917113,0.0603264043538,0.0605403277735,0.0598985575144,0.0637491790689,0.0656744898461,0.0658884132658,0.0661023366855,0.0695251114006,0.0703808050794,0.0710225753385,0.074873196893,0.0757288905718,0.0753010437324,0.0738035797945,0.0731618095354,0.0735896563748,0.0729478861157,0.0712364987582,0.0690972645612,0.0675998006234,0.0631074088098,0.0654605664264,0.0686694177218,0.0686694177218,0.0680276474628,0.0675998006234,0.0701668816597,0.0714504221779,0.0731618095354,0.0738035797945,0.0765845842505,0.0761567374111,0.0735896563748,0.0742314266339,0.0757288905718,0.0767985076702,0.0742314266339,0.0740175032142,0.072733962696,0.072092192437,0.0710225753385,0.06995295824,0.0693111879809,0.0690972645612,0.0658884132658,0.0620377917113,0.0611820980325,0.059470710675,0.0613960214522,0.0607542511932,0.0626795619704,0.0609681746129,0.0613960214522,0.0598985575144,0.0607542511932,0.0633213322295,0.0639631024886,0.0652466430067,0.0654605664264,0.0665301835249,0.0654605664264,0.0675998006234,0.0682415708825,0.0686694177218,0.0705947284991,0.0693111879809,0.0695251114006,0.0693111879809,0.0688833411415,0.0701668816597,0.0710225753385,0.0705947284991,0.0701668816597,0.0697390348203,0.0693111879809,0.0703808050794,0.0682415708825,0.0680276474628,0.0690972645612,0.0682415708825,0.0665301835249,0.0688833411415,0.0703808050794,0.072733962696,0.0759428139914,0.0755149671521,0.0763706608308,0.0778681247687,0.0785098950278,0.0782959716081,0.0782959716081,0.0744453500536,0.074873196893,0.0718782690173,0.0701668816597,0.0735896563748,0.0742314266339,0.074873196893,0.0729478861157,0.0744453500536,0.0744453500536,0.0750871203127,0.0744453500536,0.0763706608308,0.0761567374111,0.0731618095354,0.0755149671521,0.0710225753385,0.0697390348203,0.0686694177218,0.0688833411415,0.0688833411415,0.0693111879809,0.0690972645612,0.0688833411415,0.067171953784,0.065032719587,0.0684554943021,0.0693111879809,0.0682415708825,0.0697390348203,0.0688833411415,0.0693111879809,0.0695251114006,0.0697390348203,0.072092192437,0.0703808050794,0.0701668816597,0.0714504221779,0.072733962696,0.0714504221779,0.0725200392763,0.0712364987582,0.0725200392763,0.0697390348203,0.0697390348203,0.0705947284991,0.0714504221779,0.072733962696,0.0738035797945,0.0765845842505,0.0759428139914,0.0787238184475,0.0761567374111,0.0793655887066,0.0774402779293,0.0810769760641,0.080435205805,0.0761567374111,0.0742314266339,0.0757288905718,0.0757288905718,0.0733757329551,0.0755149671521,0.0757288905718,0.0785098950278,0.0778681247687,0.0782959716081,0.0785098950278,0.0793655887066,0.0767985076702,0.0772263545096,0.0778681247687,0.0782959716081,0.0772263545096,0.0774402779293,0.0759428139914,0.0759428139914,0.0791516652869,0.0821465931626,0.0821465931626,0.0832162102611,0.0817187463232,0.0823605165823,0.0821465931626,0.0782959716081,0.0785098950278,0.0772263545096,0.0793655887066,0.0778681247687,0.0787238184475,0.080435205805,0.0844997507792,0.0868529083959,0.0900617596913,0.0947680749245,0.100971854096,0.109314867464,0.112523718759,0.115518646635,0.118513574511,0.121294578967,0.121508502386,0.123647736583,0.127926204977,0.13049328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m <- 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ycorr <- 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altd  <- c(264)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('JA27-8738-Foxg1-ChIP.2x36mers.hg19-male.unique.dedup.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) : 264',bty='n')
dev.off()