# R script for Peak Model
#  -- generated by MACS
p <- c(0.0478443512562,0.0560318645209,0.0638077151075,0.0716750462892,0.0798625595539,0.0797710789587,0.0794051565782,0.0793136759831,0.0796795983636,0.0796795983636,0.079633858066,0.0797253386612,0.079954040149,0.0798625595539,0.0793136759831,0.0790849744952,0.0790849744952,0.0791307147928,0.0786275715195,0.078581831222,0.0786733118171,0.0783531297341,0.0783531297341,0.078581831222,0.0788105327098,0.0783531297341,0.078261649139,0.0780786879487,0.078261649139,0.0781701685438,0.0783073894366,0.0778499864609,0.077941467056,0.0775298043779,0.0774383237828,0.0776670252706,0.0777127655682,0.0777127655682,0.0775298043779,0.0772553625925,0.0770724014022,0.0768894402119,0.076249076046,0.0766149984265,0.0767979596168,0.0771638819974,0.0773925834852,0.0773468431876,0.0771181416998,0.0776670252706,0.0778042461633,0.0784903506268,0.0787647924122,0.0789020133049,0.0786733118171,0.0787647924122,0.0786733118171,0.0787647924122,0.0786733118171,0.0784903506268,0.0788562730074,0.0786275715195,0.0786733118171,0.0783531297341,0.0786275715195,0.0786733118171,0.0790849744952,0.0793136759831,0.0795881177685,0.0795423774709,0.0795881177685,0.079954040149,0.0799082998514,0.0797253386612,0.0796795983636,0.0794051565782,0.0791307147928,0.0789020133049,0.0792221953879,0.0790392341976,0.0782159088414,0.0778499864609,0.0778042461633,0.0781701685438,0.0780786879487,0.077621284973,0.0777127655682,0.0776670252706,0.0772553625925,0.0773468431876,0.0777127655682,0.077621284973,0.0776670252706,0.0774840640803,0.0778957267584,0.0783531297341,0.0780786879487,0.078581831222,0.0786275715195,0.0787647924122,0.0786275715195,0.078581831222,0.0789934939001,0.0791764550903,0.0789477536025,0.0789020133049,0.0790849744952,0.0786275715195,0.0791764550903,0.0788105327098,0.0794051565782,0.079633858066,0.0797710789587,0.0798168192563,0.0798625595539,0.0801370013393,0.0804114431247,0.0809145863979,0.0805029237198,0.0808231058028,0.0803199625295,0.080274222232,0.0798168192563,0.0795881177685,0.0793594162806,0.0793594162806,0.0794508968758,0.0789934939001,0.0789934939001,0.0790849744952,0.0791764550903,0.0794508968758,0.079633858066,0.0793594162806,0.0792679356855,0.0791764550903,0.078581831222,0.0786275715195,0.078581831222,0.0781244282463,0.0776670252706,0.0775755446755,0.0774840640803,0.0777127655682,0.0783073894366,0.077621284973,0.077941467056,0.077941467056,0.0776670252706,0.0780786879487,0.0783988700317,0.077941467056,0.0781701685438,0.0779872073536,0.0772553625925,0.0774383237828,0.0771638819974,0.0772096222949,0.0775755446755,0.0775755446755,0.077621284973,0.0780329476511,0.0778957267584,0.0779872073536,0.0777585058657,0.0782159088414,0.0781244282463,0.0779872073536,0.0776670252706,0.0775298043779,0.0775755446755,0.0772096222949,0.0770724014022,0.0774840640803,0.0778957267584,0.0778957267584,0.078261649139,0.0783988700317,0.0787647924122,0.0786275715195,0.0787647924122,0.0792679356855,0.0794508968758,0.0796795983636,0.079633858066,0.079633858066,0.0793136759831,0.0793594162806,0.0792679356855,0.0794051565782,0.0794051565782,0.0791764550903,0.0794051565782,0.0787190521147,0.0786275715195,0.0786733118171,0.0792221953879,0.0789934939001,0.0787647924122,0.0788105327098,0.0791764550903,0.0793594162806,0.0789934939001,0.0795423774709,0.0799082998514,0.0797253386612,0.079633858066,0.0801370013393,0.0805029237198,0.0801827416368,0.0798625595539,0.0795423774709,0.0797710789587,0.0795423774709,0.0793594162806,0.0795881177685,0.0792679356855,0.0789934939001,0.0790849744952,0.0795423774709,0.079633858066,0.0798625595539,0.079954040149,0.079954040149,0.0797710789587,0.0795423774709,0.0797710789587,0.0797710789587,0.0794966371733,0.0794966371733,0.0790849744952,0.0790849744952,0.0789020133049,0.0790849744952,0.0794508968758,0.079954040149,0.0801827416368,0.0801370013393,0.0804114431247,0.0804571834223,0.0809145863979,0.081326249076,0.0816006908615,0.0818293923493,0.0820580938371,0.0821953147298,0.0825154968128,0.0830643803836,0.0834303027642,0.083338822169,0.0838419654423,0.083659004252,0.0832016012763,0.0828356788958,0.0829728997885,0.0824240162177,0.0820123535396,0.0819208729444,0.0817379117542,0.0821495744323,0.0816006908615,0.0818293923493,0.0820580938371,0.0820123535396,0.0818751326469,0.0818751326469,0.0816921714566,0.0815092102663,0.0814177296712,0.0810060669931,0.081326249076,0.0807316252077,0.080594404315,0.0805029237198,0.0803199625295,0.0801827416368,0.0799082998514,0.0794051565782,0.0789934939001,0.0789477536025,0.0784446103293,0.078581831222,0.0784903506268,0.0786733118171,0.0785360909244,0.0788562730074,0.0789934939001,0.0795423774709,0.0799082998514,0.0803657028271,0.0805486640174,0.0808231058028,0.081326249076,0.0815549505639,0.082286795325,0.0823782759201,0.0831101206812,0.0831558609788,0.0831101206812,0.0827899385982,0.0834760430617,0.0839334460374,0.0840706669301,0.084299368418,0.084299368418,0.0841164072277,0.0840249266326,0.0842078878228,0.0847567713937,0.0853971355596,0.0848025116912,0.0848025116912,0.0848025116912,0.0848939922864,0.0846195505009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m <- 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ycorr <- 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altd  <- c(0, 42, 52, 58, 116, 169, 192, 231, 350, 584)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('33-SEP3-AP1-24581456/AP1-ChIP-seq-4d-biological-reps-1-and-2-GSM1142627/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) : 0,42,52,58,116,169,192,231,350,584',bty='n')
dev.off()