# R script for Peak Model
#  -- generated by MACS
p <- c(0.0283745904754,0.0333641596949,0.0381673369608,0.042855811486,0.0474009075854,0.0477306779649,0.047243191317,0.046655339771,0.0466983532988,0.047415245428,0.0471284885763,0.0468704074098,0.0469420966227,0.0474439211132,0.0477450158075,0.0478597185482,0.0481608132424,0.0487056512607,0.0486626377329,0.0485049214645,0.0488203540013,0.0490210837975,0.0489493945846,0.0480174348166,0.0483902187238,0.0488060161587,0.0492504892789,0.0494512190751,0.049694962399,0.0491931379085,0.0493795298621,0.0493365163344,0.0493938677047,0.0501394355191,0.050110759834,0.0493938677047,0.0491501243808,0.0493078406492,0.0491644622234,0.0492504892789,0.0492935028066,0.0492504892789,0.0494368812325,0.0493078406492,0.0498096651397,0.0500820841488,0.0499960570933,0.0501537733617,0.0502254625746,0.0503258274727,0.0499960570933,0.0494798947602,0.0496519488713,0.0495945975009,0.0485335971496,0.0486196242051,0.0484905836219,0.0481321375573,0.0478740563907,0.0488060161587,0.0486339620477,0.0494798947602,0.049107110853,0.0494512190751,0.0500677463062,0.0495515839732,0.0500820841488,0.0503545031579,0.0505408951115,0.0499673814081,0.0504405302134,0.0501681112043,0.0504978815838,0.0504118545282,0.0499960570933,0.0504835437412,0.0507129492225,0.0503545031579,0.0505265572689,0.0507416249077,0.050110759834,0.0503688410005,0.0502541382598,0.0499673814081,0.0500103949359,0.0499817192507,0.0491501243808,0.0493651920196,0.0491357865382,0.04859094852,0.0487056512607,0.0490210837975,0.0484905836219,0.0490640973253,0.049350854177,0.0497093002416,0.0497093002416,0.0498813543526,0.0497379759268,0.0501824490469,0.0507416249077,0.0501681112043,0.0508276519632,0.0505982464819,0.0502971517876,0.0499960570933,0.0507272870651,0.050282813945,0.0508993411761,0.0511000709723,0.0516735846757,0.0518886523145,0.0523331254346,0.0523474632772,0.0529639905083,0.0529926661935,0.0523761389624,0.0528779634528,0.0527202471844,0.0522470983791,0.051630571148,0.0515015305647,0.0511860980278,0.0513008007685,0.0508563276484,0.0512004358704,0.0519029901571,0.0524765038605,0.0528923012954,0.053150382462,0.0530500175639,0.0531790581471,0.053494490684,0.0536235312673,0.0540249908596,0.0540249908596,0.0538099232209,0.0537812475357,0.0537525718505,0.0542974098687,0.0545841667204,0.0551003290535,0.0544407882946,0.0539389638041,0.0542974098687,0.0543977747668,0.0547418829889,0.0545841667204,0.0547562208315,0.0542830720262,0.0545841667204,0.0543834369242,0.0555017886459,0.0560896401918,0.0561613294048,0.0567491809507,0.056878221534,0.0565771268397,0.0566488160526,0.056534113312,0.0563047078306,0.0564910997842,0.0566774917378,0.0567348431082,0.0568638836914,0.0563907348861,0.0560896401918,0.0562760321454,0.0566631538952,0.0565197754694,0.0571936540709,0.0571219648579,0.0565627889971,0.0567635187933,0.0568208701637,0.0570072621173,0.057982235413,0.0579535597279,0.0578388569872,0.05874214107,0.0581973030518,0.0585414112738,0.0586561140145,0.0583550193202,0.0577671677743,0.0577671677743,0.0569212350618,0.0571076270154,0.0566488160526,0.0566058025249,0.057050275645,0.0573226946541,0.0569355729043,0.0568638836914,0.0572079919135,0.0575377622929,0.0576668028762,0.0576811407188,0.0574947487652,0.057222329756,0.0566631538952,0.056534113312,0.0571936540709,0.0572796811264,0.0579248840427,0.0573657081819,0.0576811407188,0.0574947487652,0.0581973030518,0.0582546544221,0.0582833301073,0.0581686273666,0.057982235413,0.0581686273666,0.0576954785613,0.0583550193202,0.0578818705149,0.0582976679499,0.058570086959,0.0587994924404,0.0597171143658,0.0598031414213,0.0596024116251,0.0590145600791,0.0584410463758,0.0586131004868,0.0590432357643,0.0592296277179,0.0588998573385,0.0591866141902,0.0584267085332,0.0585270734313,0.0592009520327,0.0597171143658,0.0603479794395,0.0601902631711,0.0598604927916,0.0597888035787,0.0596310873103,0.0593013169308,0.0601329118008,0.0600182090601,0.0595307224122,0.0600182090601,0.0602046010137,0.0608928174578,0.061265601365,0.0614089797908,0.0614519933186,0.061781763698,0.0615380203741,0.0610935472539,0.0615093446889,0.0617674258554,0.0615666960592,0.0608928174578,0.0612512635224,0.0609645066707,0.0610792094114,0.06084980393,0.0608928174578,0.0617674258554,0.0615093446889,0.0614950068463,0.0618964664387,0.0621832232904,0.0621115340775,0.0624126287717,0.062885777577,0.0634449534379,0.0633876020675,0.0635309804934,0.0639611157709,0.0640041292987,0.0641618455671,0.0647783727982,0.0650221161222,0.0655239406127,0.0650794674925,0.0654379135571,0.065997089418,0.06634119764,0.0665419274362,0.0674882250468,0.0677176305281,0.0679613738521,0.0682194550186,0.0684631983425,0.0690940634163,0.0694381716383,0.0689363471478,0.0688073065646,0.0688503200923,0.0684345226574,0.0683054820741,0.0683915091296,0.0688216444072,0.0684345226574,0.0690653877311,0.0691800904718,0.0705421855173,0.0715314966557,0.0718756048777,0.0727215375902,0.0739689298951,0.0749869167186,0.0754457276814,0.0775103770136,0.0775964040691,0.0787147557907,0.0793742965496,0.0799621480956,0.0814389458818,0.0821128244833,0.08280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m <- 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ycorr <- 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altd  <- c(151)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('GSE29282-OCI-LY1_BCL6_N-3_rep2_CHIP-GSM763402.36mers.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) : 151',bty='n')
dev.off()