# R script for Peak Model
#  -- generated by MACS
p <- c(0.0484253197916,0.0564788869243,0.064532454057,0.0720144777158,0.0803797958343,0.0810032978058,0.0805356713272,0.0800680448485,0.0800160863509,0.0796523768675,0.0797562938627,0.0799641278532,0.080275878839,0.0805876298248,0.0803797958343,0.0796523768675,0.0797043353651,0.0799121693556,0.0797043353651,0.0794965013746,0.0797043353651,0.0791847503888,0.0794445428769,0.0795484598722,0.0795484598722,0.0800680448485,0.0801719618438,0.0801719618438,0.0805356713272,0.0815228827821,0.0808993808106,0.0814189657869,0.0812111317964,0.0810552563035,0.0806915468201,0.0805876298248,0.0802239203414,0.0805876298248,0.0803797958343,0.0801719618438,0.0800680448485,0.0800160863509,0.079860210858,0.0799641278532,0.0799641278532,0.0798082523603,0.0800160863509,0.0793406258817,0.0799641278532,0.0794445428769,0.0796523768675,0.0787690824077,0.0789249579006,0.0790288748959,0.0792367088864,0.079288667384,0.0789769163983,0.0789249579006,0.0781455804362,0.077470119967,0.0772103274788,0.0776259954599,0.0769505349907,0.076067240531,0.0751319875736,0.0753398215641,0.0757035310475,0.0762750745215,0.0758074480428,0.0759113650381,0.0755996140523,0.0762231160238,0.0764309500144,0.0776779539575,0.0786651654125,0.0785612484172,0.0787171239101,0.0786651654125,0.0794445428769,0.0797562938627,0.0799121693556,0.079288667384,0.0791327918911,0.0786651654125,0.0789769163983,0.0789249579006,0.0787171239101,0.0779377464456,0.0775740369622,0.0777818709528,0.0785612484172,0.0789249579006,0.0790808333935,0.0790808333935,0.078457331422,0.0787690824077,0.0789249579006,0.0794445428769,0.0793406258817,0.0792367088864,0.0789249579006,0.0785092899196,0.0786651654125,0.0786651654125,0.0786651654125,0.078872999403,0.0790288748959,0.0791327918911,0.0794965013746,0.0793406258817,0.0796004183698,0.0797043353651,0.0794965013746,0.0797043353651,0.079860210858,0.0792367088864,0.0789249579006,0.0788210409054,0.0789249579006,0.0791847503888,0.0793406258817,0.0794965013746,0.0796523768675,0.0785612484172,0.078457331422,0.0792367088864,0.0797562938627,0.0804317543319,0.080847422313,0.0811591732987,0.0805356713272,0.0803797958343,0.0805876298248,0.0818346337679,0.0820944262561,0.081263090294,0.0809513393082,0.0813150487916,0.0815228827821,0.081263090294,0.0819905092608,0.0823022602466,0.0824061772419,0.0824581357395,0.0820944262561,0.083237513204,0.083653181185,0.0833414301992,0.0833414301992,0.0837051396826,0.0834453471945,0.0833933886968,0.0831335962087,0.0831855547063,0.0837570981803,0.0827698867253,0.0823022602466,0.0815748412798,0.0811072148011,0.0813150487916,0.0813670072893,0.081263090294,0.0811072148011,0.0809513393082,0.0810552563035,0.0810032978058,0.0811591732987,0.0823022602466,0.0819385507632,0.0814709242845,0.0807435053177,0.0803797958343,0.0804837128295,0.0800160863509,0.0797562938627,0.0799641278532,0.0791847503888,0.0783014559291,0.0784053729243,0.0786651654125,0.0791327918911,0.0793925843793,0.0792367088864,0.0796004183698,0.0791847503888,0.078872999403,0.079288667384,0.0791847503888,0.0793406258817,0.078872999403,0.0794445428769,0.0789769163983,0.0786651654125,0.0787690824077,0.0792367088864,0.0797043353651,0.0796004183698,0.0796523768675,0.0791847503888,0.0789769163983,0.0785092899196,0.0793406258817,0.0800160863509,0.0798082523603,0.0791327918911,0.0786651654125,0.0786132069148,0.0787690824077,0.0796004183698,0.0795484598722,0.0797562938627,0.0793925843793,0.078872999403,0.0791847503888,0.079860210858,0.0801719618438,0.0810552563035,0.0812111317964,0.0809513393082,0.0809513393082,0.0805356713272,0.0805876298248,0.0813150487916,0.0810032978058,0.0812111317964,0.0810552563035,0.080275878839,0.0802239203414,0.0797043353651,0.0806915468201,0.0810032978058,0.0817307167727,0.0818865922656,0.0817307167727,0.0817307167727,0.0819905092608,0.08266596973,0.0825620527348,0.0827179282276,0.0824061772419,0.0827179282276,0.0823542187442,0.0821983432513,0.0823022602466,0.0821463847537,0.0819905092608,0.081678758275,0.0816267997774,0.0817826752703,0.081263090294,0.0811591732987,0.0815228827821,0.081263090294,0.0817307167727,0.0820424677585,0.0823022602466,0.0814709242845,0.0814189657869,0.0813670072893,0.0815748412798,0.0812111317964,0.0811591732987,0.0809513393082,0.0804837128295,0.0797562938627,0.0802239203414,0.0807954638153,0.0805356713272,0.0807954638153,0.0803278373366,0.0799641278532,0.0791327918911,0.079288667384,0.0793925843793,0.0796523768675,0.0788210409054,0.0792367088864,0.0791847503888,0.078872999403,0.0796004183698,0.0800160863509,0.0803797958343,0.0799121693556,0.0802239203414,0.0799121693556,0.0803278373366,0.0803797958343,0.0806915468201,0.0807435053177,0.0803797958343,0.0800160863509,0.0794965013746,0.0803797958343,0.0798082523603,0.0796523768675,0.0799121693556,0.0797043353651,0.0801719618438,0.0802239203414,0.0803278373366,0.0815228827821,0.0816267997774,0.0814709242845,0.0819385507632,0.0826140112324,0.0824581357395,0.0830816377111,0.08266596973,0.0827179282276,0.0825100942371,0.0819385507632,0.0827698867253,0.0819905092608,0.0824581357395,0.0826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m <- 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ycorr <- 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altd  <- c(0, 40, 81, 103, 135, 153, 166, 200, 239, 421, 445, 465, 521, 554, 558, 567, 575, 588)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('80-APR1-APR10-APR12-APR14-GSE94486/ARR12Ypet_6BA-GSM2476326/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) : 0,40,81,103,135,153,166,200,239,421,445,465,521,554,558,567,575,588',bty='n')
dev.off()