# R script for Peak Model
#  -- generated by MACS
p <- c(0.0408978369342,0.0475149438971,0.0544724044477,0.0612082394063,0.0682052759555,0.0683398343507,0.0682923431524,0.0683398343507,0.068553544743,0.0686643575391,0.0686168663408,0.0686010359413,0.0686801879385,0.0687118487374,0.0679519895646,0.0678332615689,0.068442731947,0.0688938983308,0.0687118487374,0.0685772903422,0.0685772903422,0.06891764393,0.0681261239584,0.0682606823535,0.0686168663408,0.0683714951496,0.0675087383805,0.0676591271751,0.0675324839796,0.0679044983663,0.0677066183734,0.0675324839796,0.068276512753,0.0684585623464,0.068862237532,0.0695904359059,0.0696379271042,0.0692659127175,0.0695825207062,0.0691867607203,0.0692105063195,0.0696062663053,0.070089093488,0.0700416022897,0.0697566550999,0.0691709303209,0.0695191991084,0.0693767255135,0.0688226615334,0.0687039335377,0.0684110711481,0.0683398343507,0.0676828727742,0.0675483143791,0.0679757351637,0.0685139687445,0.0678965831666,0.0677857703706,0.0686881031382,0.0693688103138,0.0697170791013,0.069337149515,0.0696062663053,0.0696220967047,0.0695666903067,0.069392555913,0.0696220967047,0.0693688103138,0.0690363719257,0.068862237532,0.0687989159342,0.069083863124,0.0686881031382,0.0688226615334,0.0685218839442,0.0682606823535,0.0682052759555,0.068973050328,0.0682606823535,0.0680311415618,0.0681261239584,0.0679836503635,0.0680153111623,0.0677066183734,0.0678965831666,0.0681340391581,0.068221106355,0.0673425191864,0.0677778551708,0.0680707175603,0.0683794103493,0.0685693751425,0.0680707175603,0.0683160887516,0.068442731947,0.0686881031382,0.0689572199286,0.0692184215192,0.0694875383096,0.0693213191155,0.0688226615334,0.0684585623464,0.0693450647147,0.0690680327246,0.0687910007345,0.0687118487374,0.0686643575391,0.0687593399357,0.068331919151,0.068276512753,0.0683714951496,0.0685772903422,0.0684664775462,0.0687672551354,0.0687593399357,0.0685060535447,0.0682606823535,0.0683794103493,0.0687355943365,0.068806831134,0.0686643575391,0.0686960183379,0.0684664775462,0.0684189863479,0.0682685975533,0.0681736151567,0.0678807527672,0.0678965831666,0.0676274663762,0.0672317063904,0.0674849927813,0.0675166535802,0.0674770775816,0.0671525543933,0.0670100807984,0.0673425191864,0.0677303639725,0.0677936855703,0.0674691623819,0.0671762999924,0.0669625896001,0.0667567944074,0.0667884552063,0.0667567944074,0.0668122008055,0.0668676072035,0.0669309288012,0.0675562295788,0.0678886679669,0.0680311415618,0.0683714951496,0.0684585623464,0.0688780679314,0.0688543223323,0.0687593399357,0.0685693751425,0.0684902231453,0.0683477495504,0.068553544743,0.0690205415263,0.0690917783238,0.0693688103138,0.0691788455206,0.0692738279172,0.0694558775107,0.0694796231099,0.069558775107,0.0691946759201,0.0689493047289,0.0692738279172,0.0690047111269,0.0687672551354,0.0684743927459,0.0684269015476,0.0688780679314,0.0687910007345,0.0692105063195,0.0693529799144,0.0696379271042,0.0694558775107,0.0693529799144,0.0692579975178,0.0696300119045,0.0698991286948,0.0696300119045,0.0700416022897,0.0692738279172,0.068862237532,0.0686722727388,0.0685060535447,0.0688147463337,0.069337149515,0.0695983511056,0.0699703654923,0.0703977862769,0.0702078214838,0.070730224665,0.0708964438591,0.0715929814341,0.0716721334313,0.0715850662344,0.0714346774398,0.0717037942301,0.0714742534384,0.0710626630531,0.0707539702642,0.0710864086523,0.071315949444,0.0715613206352,0.0717592006282,0.0717275398293,0.0717037942301,0.0716958790304,0.0718383526253,0.0719491654213,0.0728752437882,0.0726061269978,0.0728198373901,0.0722341126111,0.0725665509992,0.0728277525899,0.072685278995,0.0725348902003,0.0724478230035,0.0728119221904,0.0726931941947,0.0730493781819,0.0732789189737,0.0735401205643,0.0739279653504,0.074022947747,0.0740625237456,0.0742208277399,0.074553266128,0.0748857045161,0.0750756693093,0.075503090094,0.07561390289,0.0755347508928,0.0753131253008,0.0758592740812,0.0764370836605,0.0763895924622,0.0766507940528,0.0764133380613,0.0762154580684,0.0765083204579,0.0763025252653,0.0767536916491,0.0768328436463,0.0769119956435,0.0768724196449,0.0769594868418,0.077315670829,0.0784712899876,0.0783446467921,0.077371077227,0.0774027380259,0.0772919252299,0.0775293812213,0.0773394164282,0.0771019604367,0.077481890023,0.0770940452369,0.0768170132469,0.0774106532256,0.0782575795952,0.0786929155796,0.0788591347737,0.0787878979762,0.0794686051518,0.0802601251235,0.0799989235328,0.0799197715357,0.0796664851448,0.0792232339606,0.0795715027482,0.0795952483473,0.0795398419493,0.0801255667283,0.079547757149,0.0797298067425,0.0800147539323,0.0804500899167,0.0804896659153,0.0814553202806,0.0813682530838,0.0818035890682,0.0827692434336,0.0824051442466,0.0836161698032,0.0834578658089,0.0838694561941,0.0841069121856,0.0843443681771,0.0840435905879,0.0837823889972,0.0839486081913,0.0837111521998,0.0848034497606,0.084906347357,0.0858561713229,0.0865606240977,0.0870751120792,0.0880328512449,0.0888560320154,0.0900828879714,0.0907794255465,0.0915076239204,0.0917767407107,0.0926078366809,0.0933518654543,0.0939613358324,0.0951327853904,0.095528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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('Oryctolagus_cuniculus-male-liver-H3K4me3-ERR572267.50mers.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()