# R script for Peak Model
#  -- generated by MACS
p <- c(0.0117040546189,0.014212066323,0.0153267381914,0.016720078027,0.0192280897311,0.0209000975338,0.0206214295667,0.0195067576982,0.0192280897311,0.0186707537969,0.0192280897311,0.0186707537969,0.018949421764,0.0211787655009,0.0217361014351,0.0209000975338,0.0197854256653,0.021457433468,0.0211787655009,0.0209000975338,0.0200640936324,0.0197854256653,0.0195067576982,0.0175560819284,0.0156054061586,0.0150480702243,0.0150480702243,0.0153267381914,0.0153267381914,0.0158840741257,0.0158840741257,0.0169987459941,0.0169987459941,0.0169987459941,0.0186707537969,0.018949421764,0.0186707537969,0.0178347498955,0.0183920858297,0.0186707537969,0.0195067576982,0.0183920858297,0.0209000975338,0.0203427615996,0.0192280897311,0.0183920858297,0.018949421764,0.0197854256653,0.0183920858297,0.0172774139613,0.0172774139613,0.0175560819284,0.0161627420928,0.0164414100599,0.0181134178626,0.018949421764,0.0175560819284,0.0161627420928,0.0175560819284,0.0175560819284,0.016720078027,0.0181134178626,0.0181134178626,0.0181134178626,0.0164414100599,0.0161627420928,0.0178347498955,0.0186707537969,0.0172774139613,0.0172774139613,0.0195067576982,0.0172774139613,0.0164414100599,0.0175560819284,0.0181134178626,0.0197854256653,0.0195067576982,0.0197854256653,0.0200640936324,0.0206214295667,0.0192280897311,0.0192280897311,0.0195067576982,0.0183920858297,0.0169987459941,0.016720078027,0.0178347498955,0.0172774139613,0.0186707537969,0.0195067576982,0.0195067576982,0.0206214295667,0.0220147694023,0.0228507733036,0.0242441131392,0.0231294412707,0.0220147694023,0.0222934373694,0.021457433468,0.0225721053365,0.0228507733036,0.0228507733036,0.0209000975338,0.0197854256653,0.0197854256653,0.0192280897311,0.0195067576982,0.0192280897311,0.0211787655009,0.018949421764,0.0181134178626,0.016720078027,0.0175560819284,0.0183920858297,0.016720078027,0.0172774139613,0.0175560819284,0.0178347498955,0.0169987459941,0.0186707537969,0.0186707537969,0.0195067576982,0.0186707537969,0.0192280897311,0.0220147694023,0.0225721053365,0.0234081092378,0.0245227811063,0.0222934373694,0.0206214295667,0.0225721053365,0.0231294412707,0.0259161209419,0.026194788909,0.0250801170405,0.0259161209419,0.0239654451721,0.0259161209419,0.0281454646788,0.0306534763829,0.0295388045144,0.0317681482514,0.028424132646,0.0287028006131,0.0303748084158,0.0289814685802,0.0303748084158,0.0295388045144,0.0298174724815,0.0298174724815,0.0306534763829,0.0300961404487,0.0328828201198,0.0328828201198,0.03093214435,0.0314894802842,0.0314894802842,0.0303748084158,0.0287028006131,0.0273094607775,0.0289814685802,0.028424132646,0.0289814685802,0.0278667967117,0.0278667967117,0.0287028006131,0.0300961404487,0.0303748084158,0.0326041521527,0.0314894802842,0.0306534763829,0.0292601365473,0.028424132646,0.0295388045144,0.0320468162185,0.0317681482514,0.0312108123171,0.0317681482514,0.03093214435,0.0323254841856,0.0303748084158,0.0312108123171,0.0298174724815,0.0298174724815,0.0275881287446,0.028424132646,0.028424132646,0.0275881287446,0.0270307928104,0.0267521248432,0.0287028006131,0.0281454646788,0.0303748084158,0.0287028006131,0.028424132646,0.0275881287446,0.0273094607775,0.0273094607775,0.0292601365473,0.0298174724815,0.03093214435,0.0317681482514,0.0323254841856,0.0342761599554,0.0351121638568,0.0367841716595,0.0362268357252,0.0362268357252,0.0345548279225,0.0348334958896,0.0320468162185,0.0337188240212,0.0331614880869,0.0339974919883,0.0342761599554,0.0328828201198,0.0331614880869,0.0331614880869,0.0323254841856,0.0326041521527,0.0326041521527,0.0300961404487,0.0295388045144,0.0295388045144,0.03093214435,0.0317681482514,0.0328828201198,0.0345548279225,0.0365055036924,0.0362268357252,0.0384561794622,0.0387348474293,0.0395708513306,0.0378988435279,0.0376201755608,0.0378988435279,0.0387348474293,0.0384561794622,0.0384561794622,0.0384561794622,0.0362268357252,0.0390135153964,0.0376201755608,0.0395708513306,0.0392921833635,0.0373415075937,0.0365055036924,0.0367841716595,0.0373415075937,0.0365055036924,0.0367841716595,0.0351121638568,0.0376201755608,0.0395708513306,0.0387348474293,0.0423575310018,0.0454228786401,0.0445868747387,0.0434722028703,0.0448655427059,0.0473735544099,0.0490455622126,0.0473735544099,0.0443082067716,0.0459802145743,0.0459802145743,0.042914866936,0.0423575310018,0.0426361989689,0.0415215271005,0.040406855232,0.0395708513306,0.0390135153964,0.0409641911662,0.0415215271005,0.0415215271005,0.042914866936,0.0418001950676,0.045144210673,0.0482095583113,0.0501602340811,0.0526682457851,0.0535042496865,0.0526682457851,0.0535042496865,0.0529469137523,0.0526682457851,0.0554549254563,0.052389577818,0.0512749059496,0.0509962379824,0.0504389020482,0.0526682457851,0.0543402535879,0.0515535739167,0.0515535739167,0.0532255817194,0.0532255817194,0.0535042496865,0.0526682457851,0.0521109098509,0.0529469137523,0.0518322418838,0.0518322418838,0.0551762574892,0.0568482652919,0.0560122613906,0.0551762574892,0.0582416051275,0.0613069527658,0.0643723004041,0.0674376480424,0.0682736519437,0.0682736519437,0.06910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m <- 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ycorr <- 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altd  <- c(4, 118, 166, 524)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('REB1_rep4-GSM5884426.2x25mers.Spar+sacCer3.unique.dedup.MACS-2.1.0_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) : 4,118,166,524',bty='n')
dev.off()