# R script for Peak Model
#  -- generated by MACS
p <- c(0.0144349657465,0.0171168719508,0.0191677414011,0.020429814909,0.0226384435478,0.0222440455766,0.0211397312572,0.02137637004,0.0217707680112,0.0218496476054,0.0220862863881,0.0216918884169,0.02137637004,0.0221651659824,0.0217707680112,0.0227173231421,0.0227173231421,0.0226384435478,0.0227962027363,0.0223229251709,0.0229539619248,0.0228750823306,0.0235849986788,0.0237427578673,0.0243737946212,0.0232694803018,0.0238216374615,0.023348359896,0.0227173231421,0.0223229251709,0.0216130088227,0.0223229251709,0.0227173231421,0.0234272394903,0.0231906007075,0.0234272394903,0.0230328415191,0.023348359896,0.0225595639536,0.0235849986788,0.0230328415191,0.0227173231421,0.0218496476054,0.0212186108515,0.020745333286,0.0212974904457,0.0216130088227,0.0206664536918,0.0222440455766,0.0211397312572,0.0217707680112,0.021060851663,0.0217707680112,0.0216918884169,0.0226384435478,0.0231906007075,0.0231906007075,0.023663878273,0.023663878273,0.0239005170557,0.0243737946212,0.0248470721867,0.0235061190845,0.0242160354327,0.0238216374615,0.0227962027363,0.0227173231421,0.0229539619248,0.0220074067939,0.0217707680112,0.0211397312572,0.0209819720687,0.0212974904457,0.020429814909,0.0209819720687,0.0212186108515,0.0208242128802,0.021060851663,0.0216130088227,0.0220074067939,0.0219285271997,0.0220074067939,0.0231906007075,0.0232694803018,0.0221651659824,0.0222440455766,0.0219285271997,0.0217707680112,0.0223229251709,0.0222440455766,0.0224806843594,0.0217707680112,0.021060851663,0.0219285271997,0.0226384435478,0.0224018047651,0.0223229251709,0.023348359896,0.0227173231421,0.0231906007075,0.0235849986788,0.0247681925924,0.0246893129982,0.023663878273,0.0237427578673,0.0247681925924,0.0251625905636,0.0246104334039,0.0257936273176,0.0250837109694,0.0247681925924,0.0247681925924,0.0252414701579,0.0256358681291,0.0252414701579,0.0245315538097,0.0241371558385,0.0239005170557,0.0220862863881,0.023348359896,0.0235849986788,0.0229539619248,0.0232694803018,0.0227962027363,0.0237427578673,0.0238216374615,0.0245315538097,0.0250837109694,0.0257936273176,0.0249259517809,0.0241371558385,0.0253203497521,0.0247681925924,0.0264246640715,0.026266904883,0.0259513865061,0.0253992293464,0.0257147477233,0.0259513865061,0.026266904883,0.0271345804197,0.0264246640715,0.0263457844773,0.0250837109694,0.0242160354327,0.0250837109694,0.0254781089406,0.0250048313751,0.0249259517809,0.0242160354327,0.023348359896,0.0228750823306,0.023663878273,0.0231906007075,0.0231117211133,0.0225595639536,0.0221651659824,0.02137637004,0.0212186108515,0.0216130088227,0.0220862863881,0.0229539619248,0.0227173231421,0.0231117211133,0.023663878273,0.0234272394903,0.023348359896,0.023663878273,0.023663878273,0.0232694803018,0.0237427578673,0.0227962027363,0.0227173231421,0.0235061190845,0.0229539619248,0.0231117211133,0.0234272394903,0.0232694803018,0.0238216374615,0.0239005170557,0.0231117211133,0.0229539619248,0.0228750823306,0.0226384435478,0.0231906007075,0.0246104334039,0.0243737946212,0.0249259517809,0.0246104334039,0.0243737946212,0.024294915027,0.024294915027,0.0241371558385,0.0240582762442,0.0235061190845,0.0221651659824,0.0230328415191,0.0227173231421,0.0217707680112,0.0222440455766,0.0224018047651,0.0231906007075,0.0230328415191,0.0222440455766,0.023348359896,0.023663878273,0.0231906007075,0.0231906007075,0.0243737946212,0.0253203497521,0.0264246640715,0.0256358681291,0.0249259517809,0.0252414701579,0.0246893129982,0.024294915027,0.0246104334039,0.0251625905636,0.0252414701579,0.0243737946212,0.0237427578673,0.0244526742154,0.0255569885349,0.0252414701579,0.0252414701579,0.0257936273176,0.0258725069118,0.0257936273176,0.0247681925924,0.0253992293464,0.0256358681291,0.0264246640715,0.0258725069118,0.026266904883,0.0261880252888,0.0258725069118,0.0253203497521,0.0259513865061,0.0264246640715,0.0263457844773,0.0259513865061,0.0259513865061,0.0261880252888,0.0256358681291,0.0265035436658,0.0277656171737,0.0276867375794,0.02658242326,0.0261091456946,0.0260302661003,0.0264246640715,0.0248470721867,0.0259513865061,0.0269768212312,0.0259513865061,0.0247681925924,0.0245315538097,0.0254781089406,0.0261091456946,0.0254781089406,0.0252414701579,0.0257147477233,0.0241371558385,0.0245315538097,0.0250048313751,0.0246893129982,0.0247681925924,0.0241371558385,0.02397939665,0.0250837109694,0.0251625905636,0.026266904883,0.0266613028543,0.02658242326,0.0253992293464,0.0256358681291,0.0261880252888,0.0258725069118,0.026897941637,0.0261091456946,0.0256358681291,0.0243737946212,0.0252414701579,0.0246893129982,0.0259513865061,0.0257936273176,0.0255569885349,0.0248470721867,0.0240582762442,0.0241371558385,0.0250837109694,0.0265035436658,0.0267401824485,0.0270557008255,0.0273712192024,0.027213460014,0.02658242326,0.0276867375794,0.0268190620427,0.0265035436658,0.0360479745692,0.0520605322006,0.0689407653687,0.0848744434059,0.0997826867179,0.117530595423,0.136225059258,0.155550559848,0.174876060438,0.195226995752,0.204771426656,0.20745333286,0.211160673789,0.215183533096,0.220626225099,0.22267709454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m <- 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ycorr <- 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altd  <- c(9, 291)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('JA26-8738-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) : 9,291',bty='n')
dev.off()