# R script for Peak Model
#  -- generated by MACS
p <- c(0.0260511937628,0.0305463017061,0.0349290319509,0.0391278714162,0.0434186562713,0.0432449816462,0.0435412501243,0.0431939008741,0.0430304424034,0.0427546062342,0.0431326039476,0.0426933093077,0.042775038543,0.0426422285356,0.0423255277487,0.0424889862193,0.0421518531236,0.0421927177412,0.0421518531236,0.0421314208147,0.0418964492632,0.0422029338957,0.0417329907925,0.0418862331087,0.0419373138808,0.0414571546232,0.0411404538363,0.0409259145936,0.0410893730642,0.0410485084466,0.0409156984391,0.040568349189,0.0406092138066,0.0405377007257,0.0404764037992,0.0410178599833,0.0411098053731,0.0413447769246,0.0414469384688,0.0415593161674,0.0414980192409,0.0418045038734,0.0418249361822,0.041794287719,0.0418147200278,0.0415797484762,0.0415797484762,0.0414878030865,0.0410076438289,0.0411200215275,0.0412528315349,0.0411404538363,0.0414367223144,0.0417840715646,0.042039475425,0.0422744469766,0.042529850837,0.0428465516239,0.0432858462638,0.0436944924405,0.0439396801465,0.0440520578451,0.0442972455511,0.044368758632,0.0446037301836,0.0445832978748,0.0448897825073,0.0449919440514,0.045349509456,0.0453086448384,0.0454516710002,0.0457479394783,0.0461055048829,0.0460952887284,0.0465652318316,0.0472497141775,0.0478218188249,0.0483837073178,0.0485675980973,0.0488638665754,0.0494359712227,0.050202182804,0.0504984512821,0.0513872567163,0.0517550382753,0.0522045490697,0.0525927629375,0.0531648675848,0.0537369722322,0.0543192930339,0.0549424784534,0.0555758800272,0.0563523077629,0.0571900324251,0.0577314886091,0.0582218640211,0.0589880756024,0.0594988833232,0.0603161756766,0.0613990880448,0.0619098957656,0.0624309196409,0.063023456597,0.0633095089207,0.0641778820461,0.064862364392,0.0654549013482,0.0660576544588,0.0664254360178,0.0669158114298,0.0673959706874,0.0675594291581,0.0676513745478,0.0681008853422,0.0686321253718,0.0690612038573,0.0695311469605,0.0698682800563,0.0701134677623,0.0704301685492,0.071063570123,0.0717582686234,0.072483615587,0.0730148556166,0.0730352879255,0.0734235017933,0.0736073925728,0.0745983595512,0.0749967895735,0.075425868059,0.0755893265296,0.0758753788533,0.0760797019417,0.0763555381109,0.0766109419713,0.076651806589,0.0770400204568,0.0764985642727,0.0766415904346,0.0767948327508,0.0771013173833,0.0775303958688,0.0778879612734,0.0779492581999,0.0780514197441,0.078490714384,0.0782148782148,0.0783987689943,0.0790015221048,0.0786848213179,0.0784702820752,0.0783170397589,0.0783272559133,0.0784192013031,0.078490714384,0.0783170397589,0.078245526678,0.07873590209,0.0784702820752,0.0785520113105,0.0784192013031,0.0781535812883,0.0777857997293,0.0772136950819,0.0770911012289,0.0769582912215,0.0769787235303,0.0763351058021,0.075916243471,0.0757323526915,0.0758345142356,0.0755791103752,0.0752419772795,0.0754156519046,0.0753134903604,0.074690304941,0.0743429556908,0.0740262549039,0.0739956064406,0.0736482571905,0.0734132856389,0.0729535586901,0.0728411809915,0.0723508055795,0.0722077794177,0.0723201571163,0.0722077794177,0.0717684847778,0.0715232970718,0.0711350832039,0.0708898954979,0.0707468693361,0.0705323300933,0.0704914654757,0.0699091446739,0.0693881207987,0.0690816361662,0.0691429330927,0.0689999069308,0.0693268238722,0.0688057999969,0.0690203392397,0.0685810445997,0.0682132630407,0.0681723984231,0.0681111014966,0.0682541276584,0.0678556976362,0.0672529445256,0.0666604075694,0.0662721937016,0.0658635475249,0.0655979275101,0.065352739804,0.0650360390171,0.064933877473,0.0643413405168,0.0641880982005,0.0638611812592,0.0635342643179,0.0634525350825,0.063023456597,0.0628191335087,0.062410487332,0.0618996796112,0.0615318980522,0.0611539003388,0.0606124441547,0.0603876887575,0.0600709879706,0.0599688264264,0.0597338548748,0.0595703964042,0.0596112610218,0.0598258002646,0.0597542871837,0.0596316933307,0.0600301233529,0.060203797978,0.0602753110589,0.0600199071985,0.0598768810367,0.0599688264264,0.0601527172059,0.0601220687427,0.0600914202794,0.0602957433677,0.0601016364338,0.0601731495147,0.0606226603091,0.0608882803239,0.0615114657433,0.0616953565228,0.0617055726773,0.0616953565228,0.0619405442288,0.0624615681041,0.0631051858324,0.0634116704649,0.0637283712518,0.0642902597447,0.064494582833,0.0650666874804,0.0653425236496,0.0663437067825,0.067017972974,0.0673551060697,0.067630942239,0.0684380184379,0.068366505357,0.0690101230853,0.0696128761958,0.0700215223725,0.0708388147259,0.071063570123,0.0716663232336,0.072044320947,0.0732293948594,0.0744349010806,0.0757119203826,0.0766415904346,0.0775508281777,0.0783579043766,0.0796247075243,0.0806871875836,0.081432966856,0.0829449577097,0.0832310100334,0.0835374946659,0.0846408393429,0.0857033194022,0.0867862317704,0.0878997926018,0.088860111117,0.0900451850294,0.0916491212728,0.0928341951851,0.0944074829653,0.095796879966,0.0967571984812,0.0976153554522,0.0986574032027,0.100148961748,0.101129712572,0.101967437234,0.102754081124,0.103326185771,0.104449962757,0.1053592005,0.106258222089,0.107167459832,0.108117562193,0.108934854546,0.109711282282,0.11104959851,0.1116114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m <- 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ycorr <- 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altd  <- c(124, 311, 516)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('L44-Tetrahymena_thermophila-H3K27ac.2x36mers.MACS-2.0.10_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) : 124,311,516',bty='n')
dev.off()