# R script for Peak Model
#  -- generated by MACS
p <- c(0.0505971304826,0.0590357231749,0.0673107939283,0.0762313460197,0.0850012857988,0.0847689125171,0.0851734141556,0.0853971810195,0.085478941989,0.0850271050523,0.0848377638599,0.0849152216204,0.0850012857988,0.0845537520711,0.0839642124491,0.0842611338646,0.0834478273787,0.0832972150665,0.0834090984984,0.0839297867777,0.0839814252848,0.0836156525266,0.0833703696181,0.0832627893951,0.0835080723035,0.0832283637237,0.0836629878247,0.0830175064867,0.0826818561909,0.0824322700735,0.082139651867,0.0824753021627,0.0827808299961,0.0828970166369,0.0829658679796,0.0830820546205,0.083107873874,0.0833402471557,0.0832283637237,0.0829701711885,0.0828023460407,0.083051932158,0.0829572615618,0.0824236636557,0.082135348658,0.0816792085125,0.0811542170243,0.0810681528458,0.0813048293365,0.0811886426956,0.0813349517989,0.0807066832966,0.0803150912848,0.0804829164327,0.0800956276299,0.0802462399421,0.0800870212121,0.0800999308388,0.079876163975,0.0801171436745,0.0801085372567,0.0801171436745,0.080091324421,0.0799966538247,0.0803323041205,0.0802290271064,0.0800181698693,0.0796653067379,0.0796825195736,0.0795448168881,0.0794200238294,0.0794157206205,0.0792521986816,0.0788218777896,0.0789122451769,0.0787186007755,0.0790241286088,0.079820222259,0.0793124436064,0.0788347874163,0.0789767933107,0.0785852012989,0.0786067173435,0.0790026125642,0.0788218777896,0.0787315104022,0.0788390906252,0.0783097959281,0.0784474986135,0.0792349858459,0.0789208515947,0.0788390906252,0.0789853997285,0.0787487232379,0.0784690146581,0.0782237317497,0.0773071482497,0.077130716684,0.0770661685502,0.0762098299751,0.0762270428107,0.0760247919915,0.0756375031887,0.0755514390103,0.0751125117004,0.0752674272215,0.0759301213952,0.0761151593788,0.0759344246042,0.0765153578084,0.0766143316135,0.0770102268342,0.0768337952685,0.0771952648178,0.0774147284727,0.0773329675032,0.0771479295196,0.0769069498201,0.0767821567614,0.0761366754234,0.0753879170713,0.0750135378953,0.0752373047591,0.0746348555103,0.0746606747638,0.0746305523014,0.0741356832756,0.0737483944728,0.0738904003671,0.0740151934258,0.0743981790197,0.0741787153648,0.0739377356652,0.0736192982051,0.0733654088789,0.0732836479094,0.0736063885784,0.0736881495479,0.0734170473859,0.0734772923108,0.0731115195526,0.0733180735807,0.0731588548507,0.0734772923108,0.0732793447005,0.0729178751512,0.0727242307498,0.0726639858249,0.0725262831394,0.0718377697122,0.0719539563531,0.0720486269493,0.0718420729211,0.0715494547146,0.0717904344141,0.0715580611324,0.0714117520291,0.0714246616559,0.0714892097897,0.071743099116,0.0715236354611,0.0711922883742,0.0714160552381,0.0714031456113,0.071205198001,0.0712740493437,0.0711836819564,0.0708179091982,0.0710029471817,0.071041676062,0.0712439268813,0.0713084750151,0.0713256878507,0.0715838803859,0.0715150290432,0.0717043702357,0.0719324403085,0.07244452217,0.0720271109047,0.0716484285197,0.071256836508,0.0711965915831,0.0710072503906,0.0704177107686,0.0705080781559,0.0703789818883,0.0700906668907,0.0699142353249,0.0700132091301,0.0702240663672,0.0705640198719,0.0705640198719,0.0705425038273,0.0712310172545,0.0710158568085,0.0711105274047,0.0713472038953,0.0713342942686,0.0715193322521,0.0717603119517,0.0718764985925,0.0716742477733,0.0718248600855,0.0715580611324,0.0715107258343,0.0710330696442,0.0711621659118,0.0710158568085,0.0707963931536,0.0704951685292,0.0703316465902,0.0703359497991,0.0702972209188,0.0702369759939,0.0703832850972,0.0707834835268,0.0708609412874,0.0711879851653,0.0713730231489,0.0713342942686,0.0714332680737,0.0717043702357,0.0718851050103,0.0722465745596,0.0723283355291,0.0721562071723,0.0722121488883,0.0718291632944,0.071902317846,0.0720055948601,0.0719711691887,0.0715322418789,0.0715150290432,0.0710890113601,0.0709427022568,0.0711793787474,0.0710631921066,0.0716828541911,0.0718119504587,0.0722508777686,0.0725090703038,0.0728490238085,0.0727543532122,0.0726123473178,0.0731631580596,0.0734858987286,0.0735977821605,0.0730125457474,0.0729953329117,0.0729609072404,0.0726166505268,0.0724660382146,0.0726898050784,0.0729393911958,0.072440218961,0.0717129766535,0.0718420729211,0.0719754723977,0.0717603119517,0.0715365450878,0.0718076472498,0.0718851050103,0.0715709707592,0.0715752739681,0.0714504809094,0.0719281370995,0.0717732215784,0.0720959622474,0.0723197291113,0.0722164520972,0.0720744462028,0.0722465745596,0.0725176767216,0.0722465745596,0.0724660382146,0.0724789478413,0.0724316125432,0.0726510761981,0.0725564056019,0.0725219799305,0.0726424697803,0.0725650120197,0.0724832510502,0.072818901346,0.0732535254469,0.0733180735807,0.0730211521653,0.07276295963,0.0730641842545,0.0737656073084,0.0739119164117,0.0738215490244,0.074006587008,0.0743207212591,0.0738817939493,0.0741787153648,0.074432604691,0.0746434619281,0.0748973512544,0.0749317769258,0.075082389238,0.075887089306,0.0763174101981,0.0764895385549,0.0773286642943,0.0779655392145,0.0790413414445,0.0798675575571,0.0802763624046,0.0803021816581,0.0807325025501,0.0810810624726,0.0814597448576,0.081756666273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m <- 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ycorr <- 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altd  <- c(1, 266)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('Mus_musculus_domesticus-male-liver-H3K4me3-ERR572162.50mers.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) : 1,266',bty='n')
dev.off()