# R script for Peak Model
#  -- generated by MACS
p <- c(0.0199306085692,0.0235418885623,0.0271531685554,0.0306730237385,0.0343757285415,0.0350614146161,0.0356099634758,0.0349242774012,0.0346957153763,0.0350157022111,0.0342385913265,0.0340100293017,0.0338271796818,0.0335986176569,0.0340557417066,0.0331872060121,0.0332329184171,0.0342385913265,0.0345128657564,0.035198551831,0.0356099634758,0.0357013882857,0.0358385255007,0.0364327867653,0.0357471006907,0.0361127999305,0.0359756627156,0.0362042247405,0.0368441984101,0.0363413619554,0.0368899108151,0.0371641852449,0.0380784333445,0.0372556100549,0.0383984201793,0.038992681444,0.038855544229,0.0384441325843,0.038946969039,0.0391298186589,0.0398155047335,0.0401354915683,0.0392212434688,0.0394498054937,0.0390383938489,0.0392212434688,0.0394498054937,0.0399526419484,0.038855544229,0.0394040930887,0.0393583806838,0.0396326551136,0.0397697923285,0.0402269163783,0.0393126682788,0.0386726946091,0.0384441325843,0.038901256634,0.0395869427086,0.0394955178987,0.0399526419484,0.0394498054937,0.0396783675186,0.0400440667584,0.0405469032131,0.0412783016927,0.0414154389077,0.0411411644778,0.0406383280231,0.0398612171385,0.038992681444,0.0392212434688,0.038901256634,0.0391298186589,0.0397240799236,0.0396326551136,0.0396783675186,0.0395412303037,0.0402726287833,0.0405926156181,0.0399526419484,0.040729752833,0.0416897133375,0.0423296870072,0.0418725629574,0.0415982885276,0.0417354257425,0.0409126024529,0.040821177643,0.0413697265027,0.042649673842,0.0431067978917,0.0430153730818,0.0422382621972,0.0428782358669,0.0437467715614,0.044432457636,0.0459866794052,0.0457581173803,0.046352378645,0.0465352282649,0.046260953835,0.0464438034549,0.0470380647196,0.0469466399097,0.0476323259843,0.0472209143395,0.0471294895296,0.0468095026947,0.0465352282649,0.0453924181405,0.0450724313057,0.0458038297853,0.0464895158599,0.04639809105,0.0459866794052,0.0461238166201,0.0458038297853,0.0465352282649,0.0469009275047,0.0473580515545,0.0471294895296,0.0466723654798,0.0468552150997,0.0475409011744,0.0474951887694,0.0474037639594,0.0471752019345,0.0475866135793,0.0477237507943,0.0484094368689,0.0486837112987,0.0484094368689,0.0477694631992,0.0478151756042,0.048180874844,0.0491865477535,0.0492779725634,0.0496436718032,0.0502379330679,0.0507407695226,0.0506493447127,0.0509693315475,0.0513350307873,0.0507407695226,0.0503293578778,0.049963658638,0.0511978935724,0.051837867242,0.0515635928122,0.0513350307873,0.0516550176221,0.0527064029366,0.0533463766062,0.0548548859704,0.05558628445,0.0554948596401,0.0545348991356,0.0538949254659,0.0550834479953,0.0565005325495,0.0571405062192,0.0569576565993,0.0561805457147,0.055540572045,0.0554491472351,0.0570033690042,0.0577347674839,0.0582833163436,0.0564548201445,0.0557691340699,0.0569576565993,0.0561805457147,0.0569119441943,0.0572319310291,0.0576890550789,0.0571862186241,0.0581461791286,0.057414780649,0.0590147148232,0.0597004008978,0.0586947279883,0.0594718388729,0.0602946621625,0.0605232241873,0.0608432110222,0.0605689365923,0.0606146489973,0.0621231583615,0.0617117467167,0.0615746095018,0.0624431451963,0.0631745436759,0.0620774459565,0.0628088444361,0.0632659684859,0.0632659684859,0.0631745436759,0.0628545568411,0.0635859553207,0.063083118866,0.0625345700063,0.0619860211466,0.0628545568411,0.0622145831714,0.0625802824112,0.063083118866,0.0624888576013,0.0627174196262,0.0626259948162,0.0634488181058,0.0639059421555,0.0639516545605,0.0646830530401,0.0655973011396,0.0645916282302,0.0655973011396,0.0669229608839,0.0695285679675,0.0703056788521,0.0709913649267,0.0714027765715,0.0721341750511,0.0726370115058,0.0718141882163,0.0726827239108,0.0725912991008,0.0729112859357,0.0716313385964,0.0715856261914,0.0713570641665,0.0707170904968,0.0708542277118,0.0705799532819,0.0714484889765,0.0725455866959,0.0735969720103,0.0728655735307,0.0726370115058,0.0729569983406,0.0736426844153,0.0754254682093,0.075974017069,0.0764311411188,0.0781682125078,0.077893938078,0.0773453892183,0.0792653102272,0.0803624079466,0.0817794925009,0.0821909041457,0.0819623421208,0.0814137932611,0.0819166297158,0.0807281071864,0.081596642881,0.0818709173108,0.0820080545258,0.0830594398402,0.0823280413606,0.0830594398402,0.0831965770551,0.0845222367994,0.085253635279,0.0868078570482,0.0856650469238,0.0862135957835,0.0859850337586,0.0856193345188,0.0863507329984,0.087173556288,0.0868535694531,0.0869449942631,0.0860764585686,0.0865335826183,0.0887734904621,0.0898705881815,0.0903277122313,0.090876261091,0.0910591107109,0.0902362874213,0.0916076595706,0.0931161689348,0.0932990185547,0.09261333248,0.0922933456452,0.0918819340004,0.09261333248,0.0920190712154,0.0922933456452,0.09261333248,0.0936647177945,0.0935732929845,0.0955846388034,0.0961789000681,0.0971388605726,0.0986016575318,0.0992416312015,0.100795852971,0.100155879301,0.101115839805,0.10235007474,0.103721446889,0.106327053973,0.108978373461,0.112086817,0.114783848893,0.118212279266,0.122006408879,0.125160564822,0.128497570386,0.130417491395,0.132931673668,0.133297372908,0.134760169867,0.135765842777,0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m <- 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ycorr <- 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altd  <- c(260)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('BCL6_UV-ChIP-seq_repl1-GSM2754202-vs-UV_IgG_control-GSM2754205.dedup.MACS-2.1.0_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) : 260',bty='n')
dev.off()