# R script for Peak Model
#  -- generated by MACS
p <- c(0.0361190969808,0.0422540436445,0.0484532305874,0.0541224352269,0.0601931416114,0.0597113395174,0.0598398200758,0.0595989190288,0.0594543784006,0.0598398200758,0.0602092016812,0.0603376822396,0.0601770815416,0.0605625232168,0.0604179825886,0.0604179825886,0.0604340426584,0.060787364194,0.0599361804946,0.0592937777026,0.0590046964462,0.05789655163,0.0577198908622,0.0577841311414,0.0582338130958,0.0589083360274,0.0594383183308,0.0596952794476,0.0600486009832,0.0598880002852,0.0600967811926,0.0603698023792,0.0607552440544,0.0598880002852,0.0604019225188,0.0601931416114,0.0593901381214,0.0588119756086,0.0586674349804,0.058217753026,0.05789655163,0.0584425940032,0.0581053325374,0.0587637953992,0.0583944137938,0.0581535127468,0.0587959155388,0.0583462335844,0.0586353148408,0.0597273995872,0.060064661053,0.0597273995872,0.059984360704,0.0603698023792,0.0602092016812,0.059823760006,0.05950255861,0.0602895020302,0.0606749437054,0.060064661053,0.0601128412624,0.0604822228678,0.0601289013322,0.0597916398664,0.0597755797966,0.0607552440544,0.0609640249618,0.060626763496,0.059823760006,0.0596792193778,0.0599361804946,0.0598719402154,0.0602895020302,0.0601610214718,0.0598398200758,0.059904060355,0.060144961402,0.0602573818906,0.0606428235658,0.0602734419604,0.059904060355,0.0598880002852,0.0593740780516,0.0591652971442,0.0590368165858,0.0581535127468,0.0578804915602,0.0574468696756,0.057013247791,0.0575914103038,0.0580892724676,0.0585710745616,0.0590368165858,0.0596149790986,0.0599201204248,0.0603537423094,0.0606588836356,0.060867664543,0.0612209860786,0.0611406857296,0.0610925055202,0.0608997846826,0.0609800850316,0.0609319048222,0.0612209860786,0.061188865939,0.0609640249618,0.061028265241,0.0615582475445,0.0623773111043,0.0623291308949,0.0624897315929,0.0618955090103,0.0614458270559,0.0615421874747,0.0615100673351,0.0618152086613,0.0618312687311,0.0619918694291,0.0622006503365,0.0611246256598,0.0617991485915,0.0625218517325,0.0629715336869,0.0628912333379,0.0636942368279,0.0634854559205,0.0636299965487,0.0625860920117,0.0619115690801,0.0621524701271,0.0611406857296,0.0614297669861,0.0612852263579,0.0605946433564,0.0605304030772,0.0609800850316,0.0612049260088,0.0621845902667,0.0624736715231,0.0630357739661,0.0631000142453,0.0627466927097,0.0626021520815,0.0633890955017,0.0627145725701,0.0630839541755,0.0633087951527,0.0637263569675,0.0631642545245,0.0638708975957,0.0639833180843,0.0644490601085,0.0648826819931,0.0647381413649,0.0658302261113,0.0655090247153,0.0653002438079,0.0652841837381,0.0661032472979,0.0656053851341,0.0660068868791,0.0652199434589,0.0653484240173,0.0653163038777,0.0655893250643,0.0654929646455,0.0661193073677,0.0661353674375,0.0667938302993,0.0674362330914,0.067227452184,0.068110756023,0.0679662153948,0.0677253143478,0.0668741306483,0.0670829115558,0.067147151835,0.0674522931612,0.0670186712765,0.0667295900201,0.0674201730216,0.0675647136498,0.0679662153948,0.0686407383264,0.0693473813976,0.069234960909,0.0688816393734,0.0686407383264,0.0691225404204,0.069556162305,0.0693634414674,0.0696204025842,0.0690583001412,0.0683677171398,0.067950155325,0.068672858466,0.068672858466,0.0684158973492,0.068271356721,0.0681589362324,0.068110756023,0.0671150316954,0.068271356721,0.068431957419,0.068431957419,0.0682552966512,0.0694437418164,0.0692510209788,0.069395561607,0.068672858466,0.0687370987452,0.0704555262138,0.0713067099132,0.0714512505414,0.0720775932636,0.0719009324958,0.0714994307508,0.0726396957066,0.0719972929146,0.0733142186383,0.0739566214303,0.0735229995457,0.072206073822,0.0731054377309,0.072768176265,0.0738120808021,0.0735872398249,0.0729127168933,0.0735390596155,0.0732178582195,0.0728163564744,0.0722221338918,0.0728163564744,0.0731054377309,0.0736193599645,0.0729930172423,0.0733302787081,0.0738120808021,0.0748399252693,0.0754662679915,0.0752896072237,0.0760444305043,0.0765422926681,0.0772489357393,0.0777467979031,0.0785337413233,0.0792564444644,0.079609766,0.0789191829986,0.0786140416723,0.0799470274658,0.0804770097692,0.081055172282,0.0802842889316,0.0803806493504,0.0805894302578,0.0808785115142,0.0814887941666,0.0824684584244,0.0824363382848,0.0822114973076,0.0821311969586,0.0817618153532,0.082661179262,0.082661179262,0.0825969389828,0.0822114973076,0.0827896598204,0.0833196421238,0.0842511261722,0.0846526279173,0.0845562674984,0.0851986702905,0.0840423452648,0.0841547657534,0.0838496244272,0.0841226456138,0.0832714619144,0.0833196421238,0.0837532640084,0.0840584053346,0.0846847480569,0.0843314265212,0.0860337939201,0.0863549953161,0.0869973981081,0.0879128220867,0.0877040411793,0.0872222390853,0.0863710553859,0.0860016737805,0.0860016737805,0.0868367974101,0.0863068151067,0.0865637762235,0.0866280165027,0.0859856137107,0.0872864793645,0.0884749245297,0.0896312495553,0.0905627336038,0.09247388191,0.0934214260282,0.0956377156606,0.0973722031991,0.0987212490623,0.101130259532,0.103009287699,0.10453499433,0.106703103753,0.10855001178,0.107682768011,0.108887273246,0.109063934014,0.109192414572,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m <- 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ycorr <- 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altd  <- c(238)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('Macaca_mulatta-male-liver-H3K4me3-ERR572245.50mers.unique.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) : 238',bty='n')
dev.off()