# R script for Peak Model
#  -- generated by MACS
p <- c(0.0345537386476,0.0404159402873,0.0460868346475,0.0521585633078,0.0579843254658,0.0579797705306,0.0581574130045,0.0584625936648,0.0586356812035,0.0588998674468,0.0588087687422,0.0587222249729,0.0589363069287,0.0586675657501,0.0584443739239,0.0584625936648,0.0581437481988,0.0577656885748,0.057351189469,0.0571234427075,0.057014124262,0.057132552578,0.0571006680314,0.0569594650393,0.0570460088086,0.0569503551688,0.0571917667359,0.0574240684326,0.0574468431088,0.0574468431088,0.0573420795985,0.0571644371246,0.0569776847802,0.0572737555701,0.0572282062178,0.0572783105053,0.057132552578,0.0571598821893,0.0573420795985,0.057291975311,0.0577201392225,0.0578385675385,0.058048094559,0.0578932267612,0.0579023366317,0.0578340126032,0.0581528580693,0.0583760498955,0.0586356812035,0.0583806048307,0.0580526494942,0.0579706606601,0.057829457668,0.0578249027328,0.0575424967486,0.0574377332383,0.0572418710235,0.057014124262,0.056736273213,0.0571963216712,0.0572282062178,0.0576381503884,0.0577155842873,0.0579433310487,0.0584534837944,0.0586174614626,0.0586311262683,0.0587723292604,0.0590182957628,0.0586812305558,0.0588998674468,0.0586630108149,0.0586630108149,0.058366940025,0.0583623850898,0.0582940610614,0.0584899232762,0.0582895061261,0.0577246941577,0.0581710778102,0.0578977816964,0.0579433310487,0.0579251113078,0.0581847426159,0.0582120722272,0.0581209735227,0.0580617593647,0.0579979902715,0.058366940025,0.058048094559,0.0583168357375,0.0580298748181,0.0581710778102,0.0579023366317,0.0577019194816,0.0578021280566,0.057947885984,0.0581801876806,0.058048094559,0.0581710778102,0.0582029623568,0.0584489288592,0.0586402361388,0.0589727464105,0.0592278227833,0.0593781356459,0.0595284485084,0.0596559866949,0.059778969946,0.0597288656585,0.0593872455163,0.0594965639618,0.0592369326538,0.059082064856,0.0589317519934,0.0587768841956,0.0582986159966,0.0581118636522,0.0583396104137,0.0586539009445,0.0587723292604,0.0589545266696,0.0587996588718,0.0586037966569,0.058426154183,0.0586493460092,0.0588269884832,0.0594646794152,0.0594327948686,0.0592187129129,0.0594692343505,0.0590456253742,0.0590957296617,0.0590957296617,0.0588543180945,0.0589590816048,0.0590684000503,0.0585035880819,0.0584944782114,0.0586311262683,0.0585992417217,0.058804213807,0.0587951039366,0.0593234764231,0.0600887055416,0.0601706943757,0.0600294913836,0.0603164523031,0.0602526832099,0.0600021617723,0.0597425304642,0.0596650965653,0.0597607502051,0.0594236849982,0.0591640536901,0.0590957296617,0.0596332120187,0.0594464596743,0.0594737892857,0.0596742064358,0.0598154094279,0.0597926347517,0.06015702957,0.0602936776269,0.0605305342588,0.060375666461,0.0599702772257,0.0602891226917,0.0602617930803,0.0602845677565,0.0604576552952,0.0604439904895,0.0603802213963,0.0605806385463,0.0605851934816,0.0605578638702,0.0606261878986,0.0601934690519,0.0603847763315,0.0604758750361,0.0603301171088,0.0605715286759,0.0602982325621,0.0600386012541,0.0597880798165,0.059838184104,0.059838184104,0.0600750407359,0.0597926347517,0.0599475025495,0.0601114802178,0.0600203815132,0.0603483368497,0.0606307428339,0.0608266050487,0.0607355063441,0.0603984411372,0.060216243728,0.0603620016554,0.0599702772257,0.0599019531972,0.0600431561893,0.0599065081324,0.0599611673552,0.0599930519018,0.0600795956712,0.0603528917849,0.06065351751,0.0609040389476,0.0612547689602,0.061090791292,0.0611454505148,0.0612411041546,0.0614187466285,0.0614187466285,0.061309428183,0.0614961805274,0.0613914170171,0.0612547689602,0.0614460762399,0.0616601581956,0.0617284822241,0.0618560204105,0.0617193723536,0.0618560204105,0.0620017783378,0.06184691054,0.0617148174184,0.0619972234026,0.0620336628844,0.0624253873141,0.062284184322,0.0620427727549,0.061787696382,0.0616829328718,0.0620746573015,0.0622113053583,0.0625711452414,0.0626713538165,0.0624117225084,0.0624800465369,0.0624572718607,0.0626485791403,0.0627624525211,0.0631268473394,0.0631359572098,0.0635322365748,0.0635595661861,0.0634912421577,0.0635914507328,0.0636734395669,0.0639831751624,0.0640059498386,0.0641835923125,0.0642245867296,0.0643885643978,0.0644568884263,0.0643065755637,0.0642291416648,0.0642428064705,0.064251916341,0.0642382515353,0.0646436407707,0.0647802888275,0.0645889815479,0.0646208660945,0.0645343223252,0.0649761510424,0.0651902329981,0.0656001771688,0.0656138419744,0.0659326874405,0.0659281325053,0.0657960393836,0.0661649891372,0.066260642777,0.0666842517533,0.066638702401,0.0669666577375,0.0674130413899,0.0675633542525,0.0676498980218,0.0679231941356,0.0680598421924,0.068210155055,0.0681190563504,0.0679004194594,0.068369577788,0.0684606764926,0.0683422481766,0.0682010451845,0.0683422481766,0.0682784790834,0.0685563301324,0.0683058086948,0.068706642995,0.0690710378133,0.069362553668,0.069622184976,0.0702826505842,0.0714532689381,0.0722093881861,0.0736533026537,0.075110881927,0.0767643234152,0.0786364017943,0.0802898432824,0.0818157465842,0.0839383464009,0.0851818437184,0.0865528792224,0.0878328160217,0.0883702983788,0.0890353189222,0.0904245741671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m <- 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ycorr <- 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altd  <- c(162)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('GSE29282-OCI-LY1_BCL6_D-8_CHIP-GSM763404.36mers.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) : 162',bty='n')
dev.off()