# R script for Peak Model
#  -- generated by MACS
p <- c(0.0424087288038,0.0503105261365,0.0569799330595,0.0626344302333,0.0697387984773,0.0696663049238,0.0690138629422,0.0684339145142,0.0695938113703,0.0680714467466,0.0690863564957,0.0691588500493,0.0693038371563,0.0706087211195,0.0708986953335,0.071116175994,0.0722035792967,0.0736534503669,0.0732184890459,0.0735809568134,0.073943424581,0.0735809568134,0.0741609052415,0.0743058923485,0.0735809568134,0.0735809568134,0.0730010083853,0.0722760728502,0.0721310857432,0.0722760728502,0.0718411115292,0.0717686179756,0.071116175994,0.070536227566,0.0712611631011,0.0701012662449,0.0700287726914,0.0702462533519,0.0708986953335,0.070971188887,0.070681214673,0.0701012662449,0.070681214673,0.0718411115292,0.0715511373151,0.0720585921897,0.0721310857432,0.0718411115292,0.0716236308686,0.0716961244221,0.0722035792967,0.0723485664037,0.0719860986362,0.0718411115292,0.0729285148318,0.0733634761529,0.0731459954924,0.0727110341713,0.0716961244221,0.0711886695476,0.070971188887,0.0707537082265,0.0711886695476,0.07082620178,0.0698837855844,0.0701737597984,0.0707537082265,0.0722035792967,0.0732184890459,0.0733634761529,0.0731459954924,0.0732909825994,0.0732184890459,0.073943424581,0.0737259439204,0.0740159181345,0.0743058923485,0.0731459954924,0.0743058923485,0.0737259439204,0.073943424581,0.074233398795,0.0751033214371,0.0748858407766,0.0751033214371,0.0747408536696,0.0741609052415,0.0751758149907,0.073943424581,0.0752483085442,0.0752483085442,0.0751033214371,0.0747408536696,0.073943424581,0.0741609052415,0.074088411688,0.0733634761529,0.0726385406178,0.0724210599572,0.0713336566546,0.0713336566546,0.0714786437616,0.0719136050827,0.0731459954924,0.0733634761529,0.0724935535108,0.074088411688,0.0748133472231,0.074378385902,0.0760457376328,0.077350621596,0.0780755571311,0.0777130893635,0.0772781280425,0.0753932956512,0.0761182311863,0.0756832698652,0.0752483085442,0.0757557634187,0.0754657892047,0.0744508794555,0.074088411688,0.0745958665626,0.0737984374739,0.0753932956512,0.0748133472231,0.0751033214371,0.0763357118468,0.077350621596,0.0781480506846,0.0782930377916,0.0788004926662,0.0785105184521,0.0788004926662,0.0785830120057,0.0797429088618,0.0792354539873,0.077495608703,0.0765531925074,0.0764806989538,0.0771331409354,0.0766981796144,0.0757557634187,0.0764082054003,0.0762632182933,0.0765531925074,0.0764806989538,0.0765531925074,0.0777130893635,0.0766256860609,0.0752483085442,0.0756107763117,0.0766256860609,0.0761182311863,0.0769881538284,0.0764806989538,0.0774231151495,0.0781480506846,0.0771331409354,0.0777130893635,0.0785830120057,0.077350621596,0.0755382827582,0.0766981796144,0.0769881538284,0.0762632182933,0.0771331409354,0.0770606473819,0.07764059581,0.0780030635776,0.0768431667214,0.077785582917,0.0791629604337,0.0769881538284,0.0771331409354,0.0771331409354,0.0764806989538,0.0770606473819,0.0777130893635,0.0771331409354,0.0780030635776,0.0789454797732,0.0795979217548,0.0804678443969,0.0795254282013,0.0809752992715,0.0795254282013,0.0793079475408,0.0785830120057,0.0771331409354,0.0774231151495,0.0764806989538,0.0756832698652,0.0764082054003,0.0766981796144,0.0752483085442,0.0770606473819,0.077205634489,0.0767706731679,0.0777130893635,0.077205634489,0.0770606473819,0.0769881538284,0.0766256860609,0.077495608703,0.0792354539873,0.0780030635776,0.077785582917,0.0782205442381,0.0791629604337,0.0791629604337,0.0785830120057,0.0793804410943,0.0801053766294,0.0782205442381,0.0777130893635,0.0780755571311,0.0784380248986,0.0785105184521,0.0780030635776,0.07764059581,0.0774231151495,0.0778580764705,0.0771331409354,0.0778580764705,0.0769156602749,0.077350621596,0.0765531925074,0.0769881538284,0.0764082054003,0.0781480506846,0.0793804410943,0.0800328830759,0.080757818611,0.081192779932,0.0831501058768,0.0820627025742,0.0833675865374,0.0828601316628,0.0837300543049,0.0831501058768,0.0829326252163,0.0812652734856,0.0819177154672,0.0814827541461,0.0792354539873,0.0802503637364,0.0800328830759,0.080612831504,0.0817727283601,0.0813377670391,0.0814827541461,0.0816277412531,0.080612831504,0.0805403379504,0.0820627025742,0.0820627025742,0.0820627025742,0.0817727283601,0.0811202863785,0.0819902090207,0.0822801832347,0.0825701574487,0.0827876381093,0.0835850671979,0.0837300543049,0.0822801832347,0.0822801832347,0.0822801832347,0.0816277412531,0.080612831504,0.0806853250575,0.0809752992715,0.0813377670391,0.0814102605926,0.0811202863785,0.0827151445558,0.0839475349655,0.0840925220725,0.0828601316628,0.0837300543049,0.0831501058768,0.0838750414119,0.0831501058768,0.0824251703417,0.0824976638952,0.0835850671979,0.0827151445558,0.0827151445558,0.0840925220725,0.0822076896812,0.0824251703417,0.081192779932,0.0824976638952,0.084020028519,0.0835125736444,0.0821351961277,0.0816277412531,0.0814102605926,0.0821351961277,0.0836575607514,0.0834400800909,0.0832225994303,0.0819177154672,0.0826426510023,0.0830776123233,0.084310002733,0.0842375091795,0.0852524189286,0.0872097448734,0.087717199748,0.0890945772647,0.0902544741209,0.0919218258516,0.0904719547814,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m <- 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ycorr <- 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altd  <- c(4, 212)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('80-APR1-APR10-APR12-APR14-GSE94486/ARR12Ypet_mock-GSM2476325/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) : 4,212',bty='n')
dev.off()