# R script for Peak Model
#  -- generated by MACS
p <- c(0.020599758372,0.0245220960853,0.028264784743,0.0319775318915,0.0354208054565,0.0360196356418,0.0357801035677,0.0357801035677,0.0351213903639,0.0360795186603,0.035929811114,0.0359896941325,0.0358100450769,0.0361693431881,0.0368879394104,0.0368579979011,0.0371574129937,0.037995775253,0.0385347224198,0.0379358922345,0.0386844299661,0.0385047809105,0.039133552605,0.0390137865679,0.0389239620402,0.0388940205309,0.0385047809105,0.0387742544938,0.0383251318549,0.0386844299661,0.0381454827994,0.0379658337438,0.0372172960122,0.0365885243177,0.0366484073363,0.0369478224289,0.0367082903548,0.0361992846973,0.0364088752622,0.0358100450769,0.036049577151,0.0363489922437,0.0366783488455,0.0367981148826,0.036618465827,0.037187354503,0.037876009216,0.0382053658179,0.0385047809105,0.0385347224198,0.0392233771328,0.0390736695865,0.0398521488273,0.0416785808922,0.0413791657996,0.0419779959848,0.0422774110775,0.0415887563644,0.0417085224015,0.0425768261701,0.0429361242812,0.042906182772,0.0427265337164,0.0424870016423,0.0436846620128,0.0432355393738,0.0437445450313,0.0438343695591,0.0440439601239,0.0435648959757,0.0430558903183,0.0429960072997,0.043145714846,0.0422774110775,0.0422774110775,0.0419779959848,0.0413192827811,0.0424271186238,0.0424870016423,0.0427564752256,0.0433553054109,0.0439241940869,0.043025948809,0.0436247789942,0.0427265337164,0.0421576450404,0.0420977620219,0.0425169431516,0.0428762412627,0.0429660657905,0.0430558903183,0.043714603522,0.0446128487999,0.044852380874,0.0456009186055,0.0464392808648,0.0473974091612,0.0472477016149,0.0473974091612,0.0478165902909,0.0478165902909,0.0468884035038,0.0473375261427,0.0475471167075,0.0472477016149,0.0475770582168,0.0469482865223,0.0471279355778,0.0468884035038,0.0466488714297,0.0467087544482,0.0479363563279,0.0472776431242,0.0474572921797,0.0469482865223,0.0467386959574,0.0477567072723,0.0473974091612,0.0477267657631,0.0482956544391,0.0480860638742,0.0480860638742,0.048744777078,0.047606999726,0.0488046600965,0.0485052450039,0.0484753034946,0.0482657129298,0.0491340166984,0.0491340166984,0.0493436072632,0.0488944846243,0.0491639582076,0.0499424374484,0.0496130808466,0.0496130808466,0.0493735487725,0.0491340166984,0.0488046600965,0.0491340166984,0.0494933148095,0.050002320467,0.0502418525411,0.0505412676337,0.0509903902726,0.0514694544208,0.0509005657448,0.0519784600782,0.0520982261153,0.0521880506431,0.0519185770597,0.0528168223376,0.0531461789394,0.0531162374302,0.0533857110135,0.0544336638377,0.0548229034581,0.0550624355322,0.054463605347,0.0547630204396,0.055272026097,0.0542540147821,0.0541641902543,0.0538048921432,0.0535054770506,0.0526970563005,0.0532360034672,0.0530862959209,0.0537749506339,0.0545534298747,0.0552420845878,0.0549127279859,0.0546731959118,0.0560505053378,0.0563499204304,0.0569487506157,0.057218224199,0.0567391600508,0.0570086336342,0.0564696864675,0.0564696864675,0.0575775223102,0.0578469958935,0.0575475808009,0.0582062940047,0.0588650072084,0.0592542468288,0.0607213807826,0.060302199653,0.0606914392734,0.0600926090881,0.0595836034307,0.0592542468288,0.0590745977732,0.0585655921158,0.0586853581528,0.0589248902269,0.059044656264,0.0601824336159,0.0597931939955,0.0608411468197,0.0612603279494,0.0622783392642,0.0630568185051,0.0630867600143,0.062368163792,0.0620388071902,0.061559743042,0.0614998600234,0.0626076958661,0.0617992751161,0.0623382222828,0.0614998600234,0.0617094505883,0.0624280468106,0.0626675788846,0.0634161166162,0.0645239524589,0.0638951807644,0.0639850052922,0.0660509694312,0.0661108524497,0.0675779864036,0.0673085128202,0.0690151788481,0.0695541260148,0.0697038335611,0.0692547109222,0.070033190163,0.0700032486538,0.0688355297926,0.0691050033759,0.0688355297926,0.0695241845056,0.0689253543203,0.0693145939407,0.0695541260148,0.0698535411074,0.0697038335611,0.0695241845056,0.0700930731815,0.0715602071354,0.0717398561909,0.071979388265,0.0720392712835,0.0717997392095,0.0715302656261,0.0722189203391,0.0729075750521,0.0741052354226,0.074494475043,0.0736261712744,0.0734465222188,0.0730872241077,0.0736561127837,0.0743148259874,0.0749136561727,0.0741351769319,0.0752430127745,0.075183129756,0.075752018432,0.0760214920153,0.0774886259692,0.0780575146451,0.0777281580433,0.0778778655896,0.0784467542655,0.0792851165249,0.0785665203026,0.0786264033211,0.0775185674784,0.0780874561544,0.0792851165249,0.0803031278398,0.0800635957657,0.0799438297286,0.0809318995343,0.0810516655713,0.0818900278306,0.0817403202843,0.0832373957474,0.0828182146177,0.0817702617936,0.0822493259418,0.0836565768771,0.0841356410253,0.0838362259326,0.084225465553,0.0836865183863,0.0848242957383,0.0847644127198,0.0864710787477,0.0869202013866,0.0870699089329,0.0869202013866,0.0872495579885,0.0863513127106,0.0868902598773,0.0886268674145,0.0890759900534,0.0908724806091,0.0947049937946,0.0988069805635,0.101890956017,0.10461563336,0.10949609937,0.113777735194,0.119197148371,0.123778199288,0.128868255862,0.132581003011,0.134197844511,0.135395504881,0.136473399215,0.138180065243,0.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m <- 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ycorr <- 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altd  <- c(277)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('BCL6_UV-ChIP-seq_merged-vs-UV_IgG_control-GSM2754205.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) : 277',bty='n')
dev.off()