# R script for Peak Model
#  -- generated by MACS
p <- c(0.0430105160051,0.0502523070828,0.0573180059761,0.0643837048695,0.0717135420393,0.0718235996544,0.0720657264078,0.072219807069,0.0719996918387,0.0720437148847,0.0719336572696,0.0718235996544,0.0718235996544,0.0718456111775,0.0716254959471,0.0718015881314,0.0714714152859,0.0712513000556,0.0713613576707,0.071559461378,0.0713173346247,0.0714053807168,0.071559461378,0.0718235996544,0.0720657264078,0.0720217033617,0.0721757840229,0.0724179107763,0.0724619338224,0.0723298646842,0.0724399222993,0.0725940029605,0.0724179107763,0.0724839453454,0.0725719914375,0.072924175806,0.0731002679903,0.0730342334212,0.0731663025594,0.0730562449442,0.0730782564673,0.0729461873291,0.0731663025594,0.0727921066678,0.0727921066678,0.0725719914375,0.0726160144836,0.0726380260066,0.0727700951448,0.0729461873291,0.0731002679903,0.0731883140824,0.0732543486515,0.0736725675891,0.0737606136813,0.0741127980498,0.0739146943425,0.0738926828195,0.0738486597734,0.0740027404346,0.0738046367273,0.073562509974,0.0737606136813,0.073584521497,0.0732323371285,0.0731883140824,0.0731883140824,0.0736725675891,0.0736505560661,0.0731002679903,0.0732543486515,0.0736945791122,0.0734744638818,0.0732763601746,0.0732543486515,0.0729461873291,0.0732763601746,0.0728141181909,0.0724619338224,0.072924175806,0.07288015276,0.0724619338224,0.0727921066678,0.0731883140824,0.0733864177897,0.0732543486515,0.0732103256055,0.0731663025594,0.0733644062667,0.0733864177897,0.0735184869279,0.0735184869279,0.0732103256055,0.0732983716976,0.0731883140824,0.0732983716976,0.0729681988521,0.0730562449442,0.0730782564673,0.07288015276,0.072924175806,0.0727921066678,0.0725940029605,0.0723298646842,0.0723958992533,0.0721537724999,0.0720877379308,0.0721757840229,0.0724619338224,0.0725940029605,0.0723738877302,0.0729902103751,0.0732103256055,0.0730122218982,0.0734084293127,0.0738706712964,0.074266878711,0.0741348095728,0.0741568210958,0.0743769363262,0.0750813050632,0.0751913626784,0.0751913626784,0.0759397544615,0.0757416507542,0.0755435470469,0.0756756161851,0.0760938351227,0.0765340655833,0.0767101577676,0.0765120540603,0.0764240079682,0.0762479157839,0.0759617659845,0.0760718235997,0.0764900425373,0.0764460194912,0.076313950353,0.0764019964451,0.0760938351227,0.0763579733991,0.07629193883,0.0764900425373,0.0764240079682,0.0763799849221,0.076313950353,0.0766661347215,0.0762479157839,0.0759177429384,0.0759397544615,0.075653604662,0.0754995240008,0.0760498120766,0.0761378581688,0.0760718235997,0.0759397544615,0.0761378581688,0.0770843536591,0.076974296044,0.0775245841198,0.0775686071659,0.0778327454422,0.0776126302119,0.0777226878271,0.0778767684883,0.0780748721956,0.0779648145804,0.0772384343204,0.0773484919355,0.0772384343204,0.0771283767052,0.076996307567,0.0770843536591,0.0771503882282,0.0772164227973,0.0773044688895,0.0768422269058,0.0773925149816,0.0770843536591,0.076996307567,0.0768862499518,0.0771723997513,0.0770843536591,0.0769522845209,0.076974296044,0.0772164227973,0.0770623421361,0.0771283767052,0.0772824573664,0.0771063651822,0.07701831909,0.0770623421361,0.0768202153828,0.0773264804125,0.0771283767052,0.0768422269058,0.0774145265046,0.0768202153828,0.0771944112743,0.0776126302119,0.0780088376265,0.0780308491495,0.0781188952417,0.0778547569653,0.0781409067647,0.0781849298108,0.0778547569653,0.0784050450411,0.0782069413338,0.0782509643799,0.0782509643799,0.0783169989489,0.0786911948405,0.0787792409326,0.079065390732,0.079021367686,0.0793075174854,0.0797697594691,0.0800559092685,0.0802540129758,0.0805401627752,0.0804521166831,0.0801659668837,0.0802980360219,0.080408093637,0.0806061973443,0.0809583817128,0.0806942434364,0.0808703356207,0.0808483240977,0.0808043010516,0.081068439328,0.081750796542,0.081772808065,0.0815526928347,0.0815747043577,0.081728785019,0.0816407389268,0.0818388426341,0.0818608541572,0.0819268887262,0.0822570615717,0.0826532689863,0.0828953957397,0.0835117183846,0.0842160871216,0.0843041332137,0.0843261447368,0.084458213875,0.0845242484441,0.0848103982435,0.0846783291053,0.0844141908289,0.084502236921,0.0842601101677,0.0841940755986,0.0839739603683,0.0841280410295,0.0839079257992,0.0843261447368,0.0842601101677,0.0845682714901,0.0848103982435,0.0850745365199,0.0853826978423,0.0848544212895,0.085140571089,0.0852066056581,0.0854487324114,0.0853166632732,0.0856908591648,0.0859549974412,0.0860430435333,0.0854707439344,0.0852506287041,0.0853826978423,0.0851185595659,0.0853166632732,0.0854927554575,0.0857128706878,0.0856028130726,0.0856028130726,0.0856028130726,0.0860430435333,0.0861531011485,0.086505285517,0.0868574698855,0.0870115505467,0.0869895390237,0.0870115505467,0.0871216081619,0.0869455159776,0.0869895390237,0.0875398270995,0.0877819538528,0.0880460921292,0.0879580460371,0.0880681036523,0.0881341382214,0.0883322419286,0.0884422995438,0.0886844262972,0.0889265530505,0.0886844262972,0.0888605184814,0.0888164954354,0.0893007489421,0.0895868987415,0.0895428756954,0.0895648872185,0.0898730485409,0.0900931637712,0.0900931637712,0.0904453481398,0.0904233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m <- 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ycorr <- 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altd  <- c(4, 209)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('33-SEP3-AP1-24581456/SEP3-ChIP-seq-4d-biological-reps-1-and-2-GSM1142624/all.1x36mers.TAIR10.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) : 4,209',bty='n')
dev.off()