# R script for Peak Model
#  -- generated by MACS
p <- c(0.0265360560271,0.0309479973812,0.0350701031718,0.0395142484773,0.0447956965216,0.0443448412007,0.0438295779769,0.0444736570067,0.0440872095888,0.0439905977343,0.0441838214433,0.043314314753,0.0434109266075,0.0428956633837,0.0417041171786,0.041865136936,0.0414142816152,0.0408668144399,0.0407379986339,0.0409956302458,0.0403193472645,0.0412532618577,0.0414464855667,0.0421549724994,0.0416397092756,0.0413820776637,0.0425414199173,0.0423481962084,0.0423159922569,0.0422515843539,0.0426702357233,0.0427668475777,0.0436363542679,0.0424448080628,0.0437329661224,0.0437651700739,0.0429922752382,0.0444092491037,0.0459228348237,0.0468245454654,0.0467601375624,0.0462770782901,0.0459228348237,0.0468889533684,0.0471787889318,0.0471787889318,0.0478872758645,0.0481771114279,0.0467923415139,0.046534709902,0.0473076047377,0.0477584600586,0.0478228679615,0.0480160916705,0.0477906640101,0.0488855983607,0.0492076378756,0.0481449074764,0.0487889865062,0.0481127035249,0.0476940521556,0.0477906640101,0.047855071913,0.0482093153794,0.0484669469913,0.0478228679615,0.0473398086892,0.0477584600586,0.0480804995735,0.0491110260211,0.0487567825547,0.0496262892449,0.0492076378756,0.049433065536,0.0488533944092,0.0488533944092,0.0486923746518,0.0481449074764,0.0475652363496,0.0472431968347,0.0474042165922,0.0469533612713,0.0477262561071,0.0473398086892,0.0482415193309,0.0492398418271,0.0496262892449,0.0501415524688,0.0501093485173,0.0498839208569,0.0502703682747,0.0500771445658,0.0502381643232,0.0499483287598,0.0489178023122,0.0482415193309,0.0482415193309,0.0484025390884,0.0488855983607,0.0493042497301,0.0491432299726,0.049368657633,0.0484347430398,0.0497551050509,0.0492720457786,0.0491432299726,0.0497229010994,0.0499483287598,0.0504313880322,0.0498839208569,0.0499161248083,0.049561881342,0.0493042497301,0.0486923746518,0.0494652694875,0.049497473439,0.0495296773905,0.0497551050509,0.0497873090024,0.0509144473045,0.0516873421403,0.0519771777037,0.0535873752781,0.0538128029385,0.0544568819683,0.0549721451922,0.0551331649496,0.0549077372892,0.0541670464049,0.0532653357632,0.0535229673751,0.0541670464049,0.0534263555207,0.0537161910841,0.0533619476177,0.0536195792296,0.0531687239088,0.0524280330245,0.0527500725394,0.0537805989871,0.0531365199573,0.0535873752781,0.0538128029385,0.0532331318117,0.0534907634237,0.0532009278603,0.0534907634237,0.0533619476177,0.0541670464049,0.053973822696,0.0538128029385,0.0527178685879,0.0531687239088,0.0535551713266,0.0541670464049,0.0545212898713,0.0544568819683,0.0552297768041,0.0550043491436,0.0552297768041,0.055551816319,0.0562280993002,0.0576128692143,0.0581603363896,0.0579027047777,0.0573874415539,0.0579349087292,0.0587400075164,0.0584823759045,0.0587078035649,0.0590942509828,0.0590620470313,0.0577416850202,0.0576450731658,0.0574196455053,0.057065402039,0.0583535600985,0.0583535600985,0.0588044154194,0.058514579856,0.0582569482441,0.0582569482441,0.05838576405,0.0584179680015,0.0593518825947,0.0599959616245,0.0591264549343,0.0590620470313,0.0596095142066,0.05989934977,0.0599959616245,0.0597705339641,0.0591908628373,0.0587078035649,0.058321356147,0.0584823759045,0.0588366193709,0.0592230667887,0.0581281324381,0.0587078035649,0.0589976391283,0.0596095142066,0.0596739221096,0.0596095142066,0.0592552707402,0.0597061260611,0.0589010272738,0.058450171953,0.0589976391283,0.0581925403411,0.0587722114679,0.0594484944492,0.0596095142066,0.0601569813819,0.0606078367028,0.0602535932364,0.0605434287998,0.0610264880721,0.0613163236355,0.0620248105683,0.0619604026653,0.0628943172585,0.0628299093555,0.0626044816951,0.0621858303258,0.0621214224228,0.0622502382287,0.0630231330645,0.0634095804823,0.0636994160457,0.0642468832211,0.0627655014526,0.0636672120943,0.0639570476577,0.0646977385419,0.0656960610381,0.0667265874857,0.0662113242619,0.066018100553,0.065824876844,0.0640536595121,0.0640214555606,0.0637316199972,0.064568922736,0.0645367187845,0.0644723108815,0.0641180674151,0.0641824753181,0.0642790871726,0.0648265543479,0.0663079361164,0.0667265874857,0.0674350744185,0.0672096467581,0.0686910285266,0.0686910285266,0.0684656008662,0.0684978048176,0.0685622127206,0.0686910285266,0.0692062917504,0.068852048284,0.0686910285266,0.0680147455453,0.0663401400679,0.0663079361164,0.0661469163589,0.0660503045045,0.0667909953887,0.0663401400679,0.0657282649896,0.0662435282134,0.0670164230491,0.0681757653028,0.0686266206236,0.0686588245751,0.0691740877989,0.0701402063436,0.0703334300525,0.0698181668287,0.07049444981,0.0705910616644,0.0705910616644,0.0701724102951,0.0715893841606,0.0725232987538,0.0718470157725,0.0708164893249,0.0703978379555,0.0716859960151,0.0721690552874,0.0723622789964,0.0729419501232,0.073328397541,0.0729097461717,0.0744877397946,0.0757758978542,0.0768708322049,0.0774827072831,0.0784166218763,0.0797369838874,0.0815726091223,0.0835370501631,0.0865642216031,0.0896880048976,0.0907829392482,0.0936490909308,0.0963542228559,0.0998644535682,0.102956032911,0.104952677903,0.107142546605,0.107432382168,0.109042579743,0.10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m <- 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ycorr <- 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altd  <- c(208)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('GSE46663-LY1_BCL6_DMSO-GSM1133657.36mers.unique.dedup.pseudoRep1.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) : 208',bty='n')
dev.off()