# R script for Peak Model
#  -- generated by MACS
p <- c(0.0350023450938,0.0405813807236,0.0464588088587,0.0520920976713,0.0575445425412,0.057182854656,0.0567126604052,0.0570924326847,0.0570743482904,0.0575716691326,0.057526458147,0.0578248506523,0.0579604836093,0.0581684541433,0.0586838593797,0.0588737455195,0.0590545894621,0.0589279987023,0.0585120576342,0.0582317495232,0.0583945090715,0.0583945090715,0.0585572686199,0.0584125934658,0.0584578044515,0.0584125934658,0.0584216356629,0.0586476905912,0.0591811802219,0.0588737455195,0.059325855376,0.0595247837129,0.0595519103043,0.0596242478813,0.0598231762182,0.0597689230354,0.0596242478813,0.059253517799,0.0594524461359,0.0596604166699,0.0594886149244,0.0592083068133,0.0587471547596,0.0590093784764,0.0589551252937,0.0591540536305,0.0596423322756,0.0601758219063,0.0597689230354,0.0605555941858,0.0606279317629,0.0611975901821,0.0617310798129,0.0622103162608,0.0625087087661,0.0626352995259,0.0620113879239,0.0610619572252,0.0615773624616,0.0609715352539,0.0609624930567,0.0606098473686,0.060356665849,0.0601125265264,0.0601758219063,0.0603204970604,0.0605465519887,0.0614959826874,0.0609624930567,0.0613874763219,0.0615683202645,0.0617039532215,0.0618395861784,0.0621470208809,0.062083725501,0.0624725399776,0.0627257214973,0.0624002024005,0.0625177509632,0.0622374428522,0.0622374428522,0.0625267931604,0.0632049579452,0.0626985949059,0.0621922318665,0.061948092544,0.0618305439813,0.0621741474723,0.0623369070206,0.062572004146,0.0628071012714,0.0627890168772,0.0623278648235,0.0624544555833,0.0629698608198,0.0630150718054,0.0631326203681,0.0634219706763,0.0638198273501,0.0640006712927,0.0638740805329,0.0636661099989,0.0635485614362,0.0638017429558,0.06388312273,0.0641634308411,0.0643352325866,0.0639645025042,0.0636118568161,0.0640639666726,0.0641272620525,0.0642176840239,0.0640639666726,0.064091093264,0.0646336250919,0.064850637823,0.0650405239628,0.0652756210882,0.0655468870021,0.0653479586652,0.0655107182136,0.0657638997332,0.0658452795074,0.0660351656472,0.0654835916222,0.0650495661599,0.0657548575361,0.0658633639017,0.0659357014787,0.0663426003496,0.0671292715,0.0666319506578,0.0670931027115,0.0671202293029,0.0671563980914,0.0675813813566,0.0673462842312,0.067680845525,0.0678074362848,0.067888816059,0.0671925668799,0.0680696600016,0.0679701958332,0.0680696600016,0.0683770947041,0.0687749513778,0.0691185548688,0.0691908924459,0.0692813144172,0.0691456814602,0.0695797069225,0.0700408589762,0.0705200954241,0.0705381798184,0.0708456145208,0.0708184879294,0.070583390804,0.0707371081553,0.0717317498397,0.0720843955278,0.0721296065134,0.0716684544597,0.0718131296138,0.0725636319757,0.0722109862876,0.0723466192446,0.072102479922,0.071686538854,0.0715961168827,0.0716503700655,0.0715780324884,0.0718764249938,0.0719758891622,0.0715961168827,0.0717588764311,0.0717407920368,0.0719216359794,0.072789686904,0.0724189568216,0.0724912943987,0.0729253198609,0.0731242481978,0.0734497672945,0.0737662441941,0.074308776022,0.0742454806421,0.0746071685273,0.0745348309502,0.0750321517924,0.0753667130863,0.0758911605199,0.0759725402941,0.0760177512797,0.0760448778711,0.0759815824912,0.0765964518961,0.0770214351613,0.0774102496379,0.0776995999461,0.0775368403977,0.0773921652436,0.0776724733547,0.0781336254084,0.0782059629854,0.0788479589817,0.0787846636018,0.0791011405014,0.0792910266411,0.0791373092899,0.0793181532325,0.0793452798239,0.0795170815694,0.0795080393723,0.0793452798239,0.0792910266411,0.0797340943005,0.0795894191464,0.0795894191464,0.0796075035407,0.0795170815694,0.079833558469,0.0799601492288,0.0798787694546,0.0805569342394,0.0805298076481,0.0802856683255,0.0808282001534,0.0812983944042,0.0812350990243,0.0824286690455,0.0828355679164,0.0833148043644,0.0835860702783,0.0841918974861,0.084390825823,0.0848971888623,0.0852407923533,0.0850689906078,0.0863710669946,0.0862896872205,0.0857923663783,0.0861359698692,0.086533826543,0.0867056282885,0.0870401895823,0.0876460167901,0.0877906919442,0.0885140677147,0.087844945127,0.0879896202811,0.0884507723347,0.0883060971807,0.0882156752093,0.0884236457434,0.0888395868114,0.0887129960515,0.088468856729,0.0884055613491,0.0895358359905,0.0893188232593,0.0901145366068,0.0905847308576,0.0910639673056,0.0913171488253,0.0918687228502,0.0917873430761,0.0918054274703,0.0917421320904,0.0911996002625,0.091922976033,0.0922213685383,0.0921399887642,0.0929537865059,0.0935867403051,0.0936409934879,0.0947803103264,0.0950696606346,0.0959105849678,0.0963265260358,0.0970137330177,0.0967967202866,0.09744775848,0.0968600156665,0.0964259902042,0.0961456820932,0.0961547242903,0.0968328890751,0.0970589440034,0.0973392521144,0.0971131971862,0.0977190243939,0.0982615562218,0.0989216366124,0.0990934383579,0.0999524470853,0.0995636326087,0.100205628605,0.100730076039,0.101760886511,0.102610853042,0.103433692981,0.103786338669,0.104808106945,0.106101141134,0.10633623826,0.10835264822,0.109347289904,0.110360015983,0.110830210234,0.110794041445,0.111074349556,0.111933358284,0.112548227689,0.113181181488,0.114329540523,0.1142300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m <- 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ycorr <- 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altd  <- c(296)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('Cavia_porcellus-male-liver-H3K4me3-ERR572229.50mers.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) : 296',bty='n')
dev.off()