# R script for Peak Model
#  -- generated by MACS
p <- c(0.0375864940287,0.0440840647894,0.0504112074645,0.057150218013,0.0635838782416,0.0635270688798,0.0636122829226,0.0636761934546,0.0635057653691,0.0636548899439,0.0637756098378,0.0638679250508,0.0638395203699,0.0633069326027,0.0633566407943,0.0633992478156,0.0638395203699,0.0636477887737,0.0640951624982,0.0637543063272,0.0635412712202,0.0631507068576,0.0636903957951,0.0637685086676,0.0637045981355,0.063441854837,0.0632004150492,0.0632927302622,0.0628382553675,0.0628737612186,0.0622843640895,0.0625897144094,0.0619577102589,0.0617588774925,0.061652359939,0.0614251224916,0.0613470096191,0.061190783874,0.0615245388749,0.0617375739818,0.0625187027071,0.0628169518568,0.0632643255813,0.0634702595179,0.0635838782416,0.0638608238806,0.064088061328,0.0640454543066,0.0637827110081,0.0635909794119,0.0637543063272,0.0634702595179,0.0633921466454,0.0635128665393,0.0630796951553,0.0631720103683,0.0626820296224,0.0630370881339,0.0631791115385,0.0632359209003,0.0630654928148,0.0630725939851,0.0626252202605,0.062547107388,0.0625187027071,0.0624192863239,0.0623695781323,0.0622275547277,0.0622843640895,0.062270161749,0.0621210371742,0.0616665622795,0.0617162704711,0.0615032353642,0.0615884494069,0.0611836827038,0.0614606283428,0.0611481768527,0.0611481768527,0.0608215230221,0.0612120873847,0.0616239552581,0.0615813482367,0.0618156868543,0.0620500254719,0.062824053027,0.062547107388,0.0629589752614,0.0631507068576,0.063718800476,0.0635980805821,0.0634702595179,0.0639105320722,0.063626485263,0.063349539624,0.0632927302622,0.0637898121783,0.0635199677096,0.0629873799423,0.0626962319629,0.0627743448354,0.0629589752614,0.0627459401545,0.0630583916446,0.0637543063272,0.0637969133485,0.0637045981355,0.0638963297318,0.0643579057967,0.0645567385632,0.0648620888831,0.0648975947342,0.0648691900533,0.0647413689892,0.0645567385632,0.064521232712,0.0646774584571,0.0646774584571,0.0642300847326,0.064428917499,0.0642868940944,0.0640241507959,0.0647484701594,0.0653591707992,0.0654656883526,0.0656290152679,0.0656858246298,0.0653875754801,0.0656148129275,0.0659414667581,0.0657071281405,0.0658704550558,0.0655224977145,0.0649188982449,0.0649970111175,0.0650467193091,0.0649757076068,0.0657923421832,0.0659627702688,0.065415980161,0.0657923421832,0.0655864082466,0.0655793070763,0.0658917585665,0.0656219140977,0.0653023614374,0.0652952602671,0.0650609216495,0.0653378672885,0.0655367000549,0.0650467193091,0.0653378672885,0.0650254157984,0.0651035286709,0.065600610587,0.0658278480344,0.0660834901627,0.0658136456939,0.0659343655878,0.0662042100566,0.0665308638872,0.066431447504,0.0664882568658,0.0666870896322,0.0662894240994,0.0662397159077,0.0661047936734,0.0663320311207,0.0666586849513,0.0665379650574,0.0666728872918,0.0665734709086,0.0667012919727,0.0661758053757,0.0664172451635,0.0667581013346,0.0673830043148,0.0677309616561,0.0675605335706,0.0676954558049,0.0682493470829,0.0686186079349,0.0690730828296,0.0699110209168,0.0697689975122,0.069669581129,0.0693358261281,0.0688600477227,0.0689736664464,0.0691085886808,0.0689807676166,0.0694636471923,0.0695985694267,0.0695133553839,0.0696340752778,0.0699749314489,0.0706140367696,0.0708980835788,0.0708270718765,0.0707560601742,0.0704862157054,0.0700672466618,0.0699678302786,0.0705146203864,0.0709406906002,0.0712602432605,0.0714377725163,0.0724319363485,0.0729148159242,0.0731775592227,0.0738095633732,0.0743705558214,0.0743563534809,0.0743563534809,0.0745196803962,0.073802462203,0.0736888434793,0.0728580065623,0.0728082983707,0.0730142323074,0.0728864112433,0.0725526562424,0.0727372866684,0.0725597574127,0.072446138689,0.0735113142235,0.0732698744357,0.0739799914587,0.0740368008206,0.0741646218847,0.0744131628428,0.0749315482696,0.0751232798658,0.0756487664628,0.0759896226339,0.0756487664628,0.0760606343362,0.0764511986988,0.0767707513592,0.0773743508288,0.077381451999,0.0779921526388,0.0785673474275,0.0782477947671,0.0786312579595,0.0789082035985,0.0787093708321,0.0786667638107,0.0787235731725,0.0786738649809,0.0790005188115,0.0787803825344,0.0790928340245,0.0796396241322,0.0801296048781,0.080619585624,0.0809320371141,0.0809391382844,0.0810740605187,0.0813936131791,0.0816137494562,0.08203981967,0.0824232828625,0.0826221156289,0.0829274659488,0.0830481858427,0.0832186139283,0.0832541197794,0.0835168630779,0.083673088823,0.0844045093567,0.083950034462,0.0835736724398,0.0833890420138,0.0831689057367,0.0832896256306,0.0837512016955,0.084475521059,0.0851714357416,0.0852921556355,0.0850436146774,0.0857182258493,0.0860590820204,0.0867620978732,0.0868757165968,0.0873585961725,0.0872023704274,0.087436709045,0.0872804833,0.0872236739381,0.086818907235,0.0870248411717,0.0873585961725,0.0870319423419,0.0875645301092,0.0876426429817,0.0882746471322,0.0886652114949,0.0892688109644,0.0901919630944,0.0916192983106,0.0931744545911,0.0940123926782,0.0954184243838,0.0962705648115,0.0971795146009,0.0981097679011,0.0981523749225,0.0983014994973,0.0985571416256,0.0987204685409,0.0990116165203,0.099125235244,0.100012881523,0.100815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m <- 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ycorr <- 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altd  <- c(278)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('Bos_taurus-male-liver-H3K4me3-ERR572160.50mers.unique.MACS2_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) : 278',bty='n')
dev.off()