# R script for Peak Model
#  -- generated by MACS
p <- c(0.0246946541569,0.028767332722,0.0336157595853,0.0374621782301,0.041437888258,0.0423106050934,0.0415995024868,0.041825762407,0.0414055654122,0.0416318253325,0.0418904080986,0.0427308020882,0.0425368650137,0.0432479676203,0.0442822986844,0.0441530073014,0.0450580469825,0.0454135982859,0.0457691495892,0.0461570237382,0.0466741892703,0.046577220733,0.0467711578076,0.0477085203345,0.0475792289514,0.0478054888717,0.0469327720363,0.0470620634194,0.0473206461854,0.0469974177279,0.0466095435788,0.0462216694297,0.0461247008925,0.0450580469825,0.0451226926741,0.0452196612113,0.0461570237382,0.0458984409722,0.0447671413708,0.0448964327538,0.0453489525943,0.0454459211316,0.0453489525943,0.046318637967,0.0462216694297,0.0457691495892,0.0452843069028,0.0453489525943,0.0462539922755,0.0467388349618,0.0470620634194,0.0479994259463,0.047643874643,0.0469974177279,0.0467711578076,0.0469004491906,0.047773166026,0.0476115517972,0.0477408431802,0.0471590319566,0.0468358034991,0.046060055201,0.0469650948821,0.0462863151212,0.0463832836585,0.0465125750415,0.046189346584,0.0472236776481,0.0468034806533,0.0476761974887,0.0479671031005,0.0490337570104,0.048161040175,0.0484842686326,0.0485812371699,0.0482580087123,0.0479671031005,0.0475469061057,0.0479347802547,0.0477085203345,0.0471590319566,0.0456721810519,0.0467711578076,0.0469974177279,0.04644792935,0.0472883233396,0.0471590319566,0.0476761974887,0.0486782057071,0.0494216311595,0.0493893083137,0.0503266708406,0.0498741510001,0.0500680880746,0.0510377734472,0.0509084820642,0.051199387676,0.0511347419845,0.0497125367713,0.0484519457868,0.0490014341647,0.0487751742444,0.0485812371699,0.0488721427816,0.0491953712392,0.0495185996967,0.0491307255477,0.0486782057071,0.0490984027019,0.0508115135269,0.0507791906812,0.051199387676,0.0513610019048,0.0507791906812,0.0502943479949,0.0495832453883,0.0508438363727,0.0511347419845,0.0516519075166,0.0510054506015,0.0512317105218,0.0499711195373,0.0502620251491,0.0514256475963,0.0526215928892,0.0535266325704,0.0533650183416,0.0538498610279,0.0540114752567,0.0541730894855,0.0545932864803,0.0554660033157,0.0547225778633,0.0543347037143,0.0532357269586,0.0530741127298,0.0536236011076,0.0534619868789,0.0534296640331,0.0533326954958,0.0532680498043,0.054237735177,0.0550134834751,0.0557892317732,0.0560154916935,0.0559185231562,0.0548518692463,0.0556599403902,0.0553367119327,0.0548841920921,0.0553043890869,0.0545609636345,0.0545286407888,0.054237735177,0.0550781291666,0.0543347037143,0.0553043890869,0.0545286407888,0.0546902550176,0.0549488377836,0.0546902550176,0.0553367119327,0.0561771059223,0.0554660033157,0.0544639950973,0.0557569089275,0.0559831688478,0.0557569089275,0.0564680115341,0.0566296257629,0.0566619486086,0.055692263236,0.055950846002,0.0562417516138,0.0568882085289,0.0573730512152,0.0568882085289,0.0580518309761,0.0581164766676,0.0591508077318,0.0597649418011,0.0608639185568,0.0600881702587,0.0607669500195,0.0605083672535,0.0596356504181,0.0595710047266,0.058989193503,0.0581164766676,0.0566942714544,0.0562740744596,0.0564680115341,0.0567589171459,0.0554983261614,0.0555952946987,0.0565003343798,0.0566296257629,0.0565326572256,0.0573730512152,0.0585366736624,0.05779324821,0.0584397051251,0.0589568706572,0.060573012945,0.0607992728653,0.0611225013228,0.0614134069346,0.0618659267752,0.062027541004,0.0621245095412,0.0641931716695,0.0643224630526,0.0637729746747,0.0635790376002,0.0638052975205,0.0640962031323,0.0633851005257,0.0634820690629,0.0633204548342,0.0635143919087,0.0620598638497,0.060960887094,0.0610255327855,0.0610255327855,0.0609285642483,0.0600881702587,0.0609932099398,0.0614134069346,0.0617043125464,0.06228612377,0.06228612377,0.0629649035309,0.0632558091426,0.0634497462172,0.0631265177596,0.0639669117493,0.0640315574408,0.0634497462172,0.062544706536,0.0617689582379,0.0628356121478,0.0624800608445,0.0625123836903,0.0631911634511,0.063999234595,0.0633851005257,0.0639022660577,0.0642254945153,0.0652598255795,0.0651951798879,0.0649042742762,0.0656476997285,0.0661648652606,0.0657769911115,0.0666497079469,0.0665204165639,0.0680719131601,0.0688153386125,0.0700436067512,0.0705607722833,0.0712395520441,0.0707223865121,0.0701728981342,0.0697850239852,0.0698819925224,0.0710779378154,0.0702375438257,0.0701082524427,0.0702375438257,0.070334512363,0.0697203782937,0.0703021895172,0.0719829774965,0.0727910486404,0.0724678201828,0.071659749039,0.0716274261932,0.0722415602626,0.0731789227894,0.073243568481,0.0737930568588,0.0745041594654,0.0738900253961,0.0741809310079,0.0745688051569,0.0758293961414,0.0758293961414,0.0758940418329,0.0737930568588,0.0739223482418,0.0733082141725,0.0734698284012,0.0733405370182,0.0733082141725,0.0728556943319,0.0718213632677,0.0718536861135,0.0710779378154,0.072047623188,0.0724678201828,0.0747627422314,0.076669790131,0.0805808544674,0.0828111308245,0.0849121157985,0.0889847943637,0.0933807013864,0.0973564114142,0.101461412825,0.105049248704,0.107925981976,0.110414841099,0.10980070703,0.112030983387,0.114616811047,0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m <- 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ycorr <- 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altd  <- c(206)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('GSE46663-LY1_BCL6_DMSO-GSM1133657.36mers.unique.dedup.pseudoRep2.dedup.pseudoRep2.MACS-2.1.0.p1e-1_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) : 206',bty='n')
dev.off()