# R script for Peak Model
#  -- generated by MACS
p <- c(0.0507420438619,0.0594730692402,0.0680034218578,0.0765865830967,0.0852507175547,0.0848599337576,0.0845712466281,0.085190867784,0.0854232257175,0.0854619520397,0.0858844210096,0.0856062956044,0.0855147606609,0.0853528142225,0.0852964850265,0.085219032382,0.0852155118073,0.0847085490433,0.0844550676614,0.0849057012293,0.0846381375484,0.0846557404221,0.0846170140999,0.0842015862794,0.0839938723692,0.0841030101865,0.0838213642065,0.08377207616,0.0835749239741,0.0830292348879,0.0830292348879,0.0829940291404,0.0827792740807,0.0831418932799,0.0830538789112,0.0828602473,0.0829729056919,0.0828074386787,0.0830750023597,0.0827159037352,0.082465942928,0.0823180787886,0.0824201754563,0.0822195026956,0.0819343361409,0.0815505934932,0.0816104432639,0.0815224288952,0.0816104432639,0.0820822002804,0.0823004759148,0.0821314883268,0.0819589801641,0.0815611552175,0.0817899925762,0.0823145582138,0.0821420500511,0.0819660213136,0.0815294700447,0.0812654269385,0.0807338201514,0.0809133694636,0.0812267006163,0.0815470729185,0.081413291078,0.0810717953273,0.0810260278556,0.0810717953273,0.0809732192343,0.0810471513041,0.0812971121113,0.0810999599253,0.0807443818756,0.0805437091149,0.0801036372712,0.0804240095734,0.080247980836,0.080205733939,0.080107157846,0.0797727032448,0.0793185491021,0.0789101624312,0.0790861911687,0.078970012202,0.0793009462284,0.0790439442717,0.0787517365675,0.0785862695543,0.0781532388601,0.0783151852986,0.0785017757603,0.0787763805907,0.0783363087471,0.0784454465643,0.0781743623086,0.0776850024185,0.0779983335711,0.0779067986277,0.0784243231158,0.0781215536874,0.0777413316144,0.0778011813852,0.0778575105812,0.0775265765547,0.0776709201195,0.0776814818437,0.077354068392,0.0773188626445,0.0769421611464,0.0770231343656,0.0769808874686,0.0769280788474,0.0768013381564,0.0767238855119,0.0763683074622,0.0765302539007,0.0762908548177,0.076259169645,0.0764035132097,0.0761922787247,0.0764844864289,0.0759880853893,0.0757662891801,0.076005688263,0.0757909332033,0.0753191761869,0.0756993982598,0.0754459168779,0.0753438202102,0.0751325857252,0.0749354335392,0.0753121350374,0.0753684642334,0.0755620958446,0.0758472623993,0.0758965504458,0.0756853159608,0.0754987254991,0.0757346040073,0.0758824681468,0.075991605964,0.0754107111304,0.0752910115889,0.074924871815,0.0748755837685,0.0749424746887,0.074784048825,0.0746397052603,0.0745974583633,0.0746115406623,0.0744953616956,0.0744812793966,0.0742946889349,0.0740693721509,0.0738405347922,0.0736856295032,0.0737560409982,0.0742031539914,0.0737666027225,0.073590573985,0.0731469815666,0.0732420370848,0.0730836112211,0.0732420370848,0.0731117758191,0.0730941729453,0.0731997901878,0.0727174714472,0.0727632389189,0.0729111030584,0.0731540227161,0.0733335720283,0.0735835328355,0.0731469815666,0.0729568705301,0.0726541011017,0.072354852248,0.0727421154704,0.0726928274239,0.0726153747794,0.0728230886897,0.072495675238,0.0725414427097,0.0726857862744,0.0728160475402,0.0731610638656,0.0729639116796,0.0727033891482,0.0723478110985,0.0721260148893,0.0717563545406,0.0719464655771,0.0717704368396,0.0718830952316,0.0718091631618,0.0714993525839,0.0715627229294,0.0718936569558,0.072199946959,0.0723161259257,0.0723900579955,0.0722914819025,0.07218586466,0.0718478894841,0.0721119325903,0.072101370866,0.072411181444,0.0721084120155,0.0722738790288,0.0718795746568,0.0717317105174,0.0716753813214,0.0716401755739,0.0719535067266,0.0720802474175,0.0722914819025,0.0722633173045,0.0723618933975,0.072383016846,0.0728054858159,0.0729603911049,0.0728512532876,0.0728758973109,0.0727209920219,0.072143617763,0.0719535067266,0.0715592023546,0.0714606262617,0.0713303649959,0.071090965913,0.07085156683,0.0705840031491,0.0707283467138,0.0705523179763,0.0711226510857,0.0710240749927,0.0711543362585,0.0709571840725,0.0709149371755,0.0707072232653,0.070837484531,0.071076883614,0.070936060624,0.0713690913182,0.0714078176404,0.0720309593711,0.0720802474175,0.0722316321318,0.072383016846,0.0726963479987,0.0727350743209,0.0726752245502,0.0723583728227,0.0721189737398,0.0718619717831,0.0712775563747,0.0712247477535,0.0713726118929,0.0712986798232,0.0713866941919,0.0715627229294,0.0715592023546,0.0720450416701,0.0720978502913,0.072298523052,0.0728653355866,0.0730519260484,0.0729674322544,0.0728019652412,0.0728336504139,0.0726118542047,0.0728125269654,0.0727456360452,0.0730237614504,0.0729287059321,0.0727421154704,0.0726259365037,0.0727773212179,0.0727385948957,0.0725027163875,0.0727597183442,0.0728653355866,0.0725484838592,0.072157700062,0.0723020436268,0.0722914819025,0.0725484838592,0.0726505805269,0.0729392676564,0.0733969423738,0.0732913251313,0.0733300514536,0.0738651788154,0.0740764133004,0.0741080984732,0.0741785099681,0.0740728927257,0.0740588104267,0.0744742382471,0.0745024028451,0.0748016516988,0.0747488430775,0.0750586536555,0.0756113838911,0.0758472623993,0.0762239638975,0.0767661324089,0.0771146693091,0.0770020109171,0.0775019325315,0.0779912924216,0.078561625531,0.0787341336938,0.0788960801322,0.07908971174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m <- 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ycorr <- 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altd  <- c(0, 260)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('Rattus_norvegicus-male-liver-H3K4me3-ERR572264.50mers.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) : 0,260',bty='n')
dev.off()