# R script for Peak Model
#  -- generated by MACS
p <- c(0.0431679286725,0.0510413244681,0.0585527250547,0.0645256460031,0.0729420346122,0.0739375214369,0.0733040298212,0.0735755262279,0.0735755262279,0.0744805142504,0.0737565238324,0.0741185190414,0.0745710130526,0.0752950034706,0.0740280202392,0.0719465477874,0.0728515358099,0.0729420346122,0.0735755262279,0.0727610370077,0.0725800394032,0.069955574138,0.0685980921043,0.0690505861155,0.0697745765335,0.0708605621605,0.0704985669515,0.0698650753357,0.069593578929,0.0687790897087,0.068869588511,0.0708605621605,0.0705890657537,0.0705890657537,0.0697745765335,0.0695030801267,0.06923158372,0.0687790897087,0.0678741016863,0.0680550992908,0.0687790897087,0.0679646004885,0.068507593302,0.0689600873132,0.0685980921043,0.0682360968953,0.0683265956975,0.0686885909065,0.0683265956975,0.067783602884,0.067059612466,0.0679646004885,0.067783602884,0.0671501112683,0.0672406100705,0.0668786148615,0.0680550992908,0.069593578929,0.069955574138,0.0714035549739,0.0714940537762,0.0714940537762,0.0707700633582,0.0720370465897,0.0730325334144,0.0734850274257,0.0726705382054,0.0717655501829,0.0720370465897,0.069955574138,0.06923158372,0.0696840777312,0.0708605621605,0.0687790897087,0.0693220825222,0.0700460729402,0.0691410849177,0.0694125813245,0.0697745765335,0.0702270705447,0.0712225573695,0.0709510609627,0.0712225573695,0.0704985669515,0.0689600873132,0.0686885909065,0.0704080681492,0.070679564556,0.0713130561717,0.0726705382054,0.0734850274257,0.0724895406009,0.0723085429964,0.0739375214369,0.0755664998774,0.0746615118549,0.0734850274257,0.0723085429964,0.0725800394032,0.0720370465897,0.0704985669515,0.070679564556,0.070317569347,0.0693220825222,0.067783602884,0.0684170944998,0.0689600873132,0.0707700633582,0.0697745765335,0.069955574138,0.0714035549739,0.0715845525784,0.0708605621605,0.0715845525784,0.0717655501829,0.0704080681492,0.0704985669515,0.070317569347,0.0701365717425,0.0700460729402,0.0690505861155,0.0694125813245,0.0704080681492,0.0708605621605,0.071041559765,0.0717655501829,0.0709510609627,0.069955574138,0.0704080681492,0.0716750513807,0.0725800394032,0.0721275453919,0.0712225573695,0.0704080681492,0.0712225573695,0.0724895406009,0.0739375214369,0.0756569986796,0.0752045046684,0.0740280202392,0.0733040298212,0.0734850274257,0.0753855022729,0.0749330082616,0.0739375214369,0.0742090178436,0.0728515358099,0.070317569347,0.0711320585672,0.0714035549739,0.0713130561717,0.0705890657537,0.0680550992908,0.0684170944998,0.0682360968953,0.0667881160593,0.0691410849177,0.0698650753357,0.0698650753357,0.0700460729402,0.0705890657537,0.0694125813245,0.0712225573695,0.0724895406009,0.0730325334144,0.0751140058661,0.0742090178436,0.0754760010751,0.0754760010751,0.0746615118549,0.0739375214369,0.0753855022729,0.0742995166459,0.0734850274257,0.0730325334144,0.0713130561717,0.0702270705447,0.068869588511,0.0693220825222,0.0693220825222,0.0691410849177,0.0694125813245,0.0705890657537,0.0719465477874,0.0725800394032,0.0725800394032,0.0723990417987,0.0732135310189,0.0712225573695,0.0719465477874,0.0714940537762,0.0712225573695,0.070317569347,0.068145598093,0.0671501112683,0.0671501112683,0.0676931040818,0.067421607675,0.0687790897087,0.0689600873132,0.069955574138,0.0698650753357,0.0705890657537,0.0723990417987,0.0728515358099,0.0731230322167,0.0723990417987,0.0717655501829,0.0714035549739,0.0718560489852,0.0716750513807,0.0727610370077,0.0721275453919,0.0704080681492,0.0693220825222,0.0698650753357,0.069955574138,0.069955574138,0.070317569347,0.0683265956975,0.067421607675,0.0667881160593,0.067059612466,0.0671501112683,0.0679646004885,0.0675121064773,0.067421607675,0.0676026052795,0.0669691136638,0.068869588511,0.0685980921043,0.0690505861155,0.06923158372,0.0711320585672,0.0708605621605,0.0714940537762,0.0727610370077,0.0723990417987,0.0732135310189,0.0728515358099,0.0745710130526,0.0736660250302,0.0741185190414,0.0728515358099,0.0738470226347,0.0733945286234,0.0740280202392,0.0748425094594,0.0741185190414,0.0736660250302,0.0727610370077,0.0742090178436,0.0743900154481,0.0742090178436,0.0749330082616,0.0766524855044,0.0765619867021,0.0761999914931,0.0771049795156,0.0778289699336,0.0794579483741,0.0781909651426,0.0775574735268,0.0789149555606,0.0784624615493,0.0770144807133,0.0746615118549,0.0753855022729,0.0747520106571,0.0742995166459,0.0739375214369,0.0748425094594,0.0757474974819,0.0743900154481,0.0733945286234,0.0724895406009,0.0721275453919,0.0712225573695,0.0730325334144,0.0723990417987,0.0716750513807,0.0712225573695,0.0707700633582,0.0722180441942,0.0736660250302,0.0736660250302,0.0758379962841,0.0763809890976,0.0763809890976,0.0771954783178,0.0763809890976,0.0756569986796,0.0759284950864,0.0755664998774,0.0745710130526,0.0758379962841,0.0759284950864,0.0758379962841,0.0743900154481,0.0743900154481,0.0764714878999,0.0771049795156,0.0777384711313,0.0786434591538,0.0803629363965,0.0811774256168,0.0813584232213,0.0815394208258,0.0831683992662,0.083801890882,0.082715905255,0.0822634112438,0.0822634112438,0.081267924419,0.081448922023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m <- 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ycorr <- 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altd  <- c(125)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('48-PIF1-PIF4-GSE43286/PIF1-peaks-3-GSM1059959/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) : 125',bty='n')
dev.off()