# R script for Peak Model
#  -- generated by MACS
p <- c(0.0340490805789,0.0395511867979,0.0451172709963,0.0505298080443,0.0566588984604,0.0565053513101,0.056786854419,0.0564669645225,0.0566461028646,0.0563901909474,0.0567740588231,0.0573370650409,0.0572602914658,0.0571195399113,0.0565437380977,0.0571195399113,0.05687642359,0.0569531971652,0.0566844896521,0.0566461028646,0.0562878261805,0.0564029865433,0.0565821248853,0.0566461028646,0.0569787883569,0.0566844896521,0.0562622349888,0.056339008564,0.0565437380977,0.0563901909474,0.0568508323983,0.0567100808439,0.0570427663362,0.0578105020877,0.0574522254036,0.0573498606368,0.0576697505332,0.0581815743676,0.0585270554557,0.0590900616735,0.0589237189273,0.0589876969066,0.0591540396528,0.0591028572694,0.0592819956114,0.0591284484611,0.0592819956114,0.0590004925025,0.0589493101191,0.0592052220362,0.0597042502747,0.0593971559741,0.0589749013108,0.0589109233315,0.0591796308445,0.0596914546788,0.0602288697049,0.0603696212593,0.0607662847309,0.061214130586,0.0610733790315,0.0611757437984,0.0615340204824,0.0612909041611,0.0612653129694,0.0608814450937,0.0605871463889,0.0602288697049,0.0599601621919,0.0589876969066,0.0586678070102,0.058770171777,0.0588085585646,0.0590644704818,0.0593459735907,0.0597042502747,0.0589237189273,0.0594483383575,0.0599729577877,0.0605743507931,0.0605487596013,0.0600241401711,0.0597554326581,0.0598066150416,0.0596658634871,0.0598322062333,0.0603568256635,0.0602416653007,0.0600881181504,0.0599345710001,0.06030564328,0.0608942406895,0.0610221966481,0.0603696212593,0.0605487596013,0.0607278979434,0.0611501526067,0.0616875676327,0.06157240727,0.0608430583061,0.061124561415,0.0611885393942,0.0613676777363,0.0623913254049,0.0619690707416,0.0615596116741,0.0613292909487,0.0607023067516,0.0602800520883,0.0609198318812,0.0611501526067,0.0613804733321,0.0617259544203,0.061930683954,0.062020253125,0.062109822296,0.062109822296,0.0624680989801,0.0628519668558,0.0633126083067,0.0632614259233,0.0629927184103,0.0623017562339,0.0619050927623,0.0621226178919,0.0626600329179,0.063018309602,0.0631846523481,0.0637092717783,0.0633893818819,0.0629415360268,0.0633893818819,0.0639651836955,0.0642338912085,0.0646049634884,0.0639651836955,0.0645793722967,0.064912057789,0.0646945326594,0.0648608754056,0.0650144225559,0.0649760357683,0.0644386207422,0.0649888313642,0.0646945326594,0.0651551741103,0.0642466868044,0.0636708849908,0.0632230391357,0.0633254039026,0.0643490515712,0.0647201238511,0.0662172085665,0.0655518375819,0.0657821583074,0.0660380702245,0.0666650544216,0.0672152650435,0.0681493435411,0.067893431624,0.067893431624,0.0674711769607,0.0668569883595,0.0669209663388,0.066626667634,0.0669721487222,0.0671129002766,0.0671001046808,0.0670617178932,0.068072569966,0.0673944033855,0.0677270888778,0.0676375197068,0.068341277479,0.0685715982045,0.0687891233341,0.06843084665,0.0689170792926,0.0686483717796,0.0682772994997,0.0688019189299,0.0695312678938,0.069966318153,0.0697487930234,0.0705805067542,0.0705549155625,0.0707084627128,0.0694800855104,0.0696208370648,0.069787179811,0.0698127710027,0.069608041469,0.0690706264429,0.070235025666,0.0701838432826,0.0702990036453,0.0707980318838,0.0716553368063,0.0723079121951,0.072410276962,0.0727045756667,0.0729221007963,0.0737922013146,0.0733187642679,0.0733187642679,0.0726917800708,0.0729860787756,0.0733827422472,0.0729860787756,0.0730116699673,0.0733571510555,0.0733315598637,0.0727045756667,0.0721671606406,0.0727557580501,0.0732291950969,0.0732291950969,0.0737410189312,0.074124886807,0.0745855282579,0.0749438049419,0.075020578517,0.0757371318851,0.0763001381029,0.075749927481,0.0761721821443,0.076466480849,0.0756859495017,0.0753020816259,0.0751485344756,0.0750717609005,0.0759546570147,0.0766200279993,0.0766840059786,0.0780531347354,0.0786545277408,0.078910439658,0.0799212917308,0.0805738671195,0.0806634362905,0.0810984865497,0.0809577349953,0.0815847191923,0.0824420241148,0.0825443888817,0.0826339580527,0.0823908417314,0.082250090177,0.0826339580527,0.0834272849959,0.0830434171202,0.0827107316279,0.0820709518349,0.0818918134929,0.0805994583112,0.0805098891402,0.0817254707468,0.0821861121977,0.0824036373273,0.082339659348,0.0828642787782,0.0836448101255,0.0846300710066,0.0848987785196,0.0864726368102,0.0870228474321,0.0867541399191,0.0874195109037,0.0876370360333,0.0875474668623,0.0876114448416,0.0876370360333,0.0869588694528,0.0868053223025,0.0866901619398,0.0869716650487,0.0869844606445,0.0859224261883,0.0854617847374,0.0861015645303,0.086485432406,0.086485432406,0.0866773663439,0.0873811241161,0.0872019857741,0.0866389795563,0.0869972562404,0.0873811241161,0.08811047308,0.0880592906966,0.0885967057227,0.0889165956191,0.0893004634949,0.0893388502824,0.0892492811114,0.0900170168629,0.0902729287801,0.091002277744,0.0919491518375,0.0929855951021,0.0933438717861,0.0946874093512,0.0959029909577,0.0975664184193,0.0996265093525,0.102134446141,0.103567552877,0.106267423603,0.107355049251,0.10779009951,0.108519448474,0.108468266091,0.109095250288,0.109044067904,0.1090568635,0.1086602000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m <- 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ycorr <- 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altd  <- c(259)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('Sarcophilus_harrisii-female-liver-H3K4me3-ERR572296.50mers.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) : 259',bty='n')
dev.off()