# R script for Peak Model
#  -- generated by MACS
p <- c(0.0486360719626,0.0566688683641,0.0646702866547,0.0727658392782,0.0811124167892,0.0811124167892,0.0810810386782,0.0813948197877,0.0814261978986,0.0815830884533,0.0817086008971,0.0818968695628,0.0819282476737,0.0821478944503,0.0819910038956,0.0813320635658,0.0813006854548,0.080641745125,0.0806103670141,0.0802965859046,0.0806103670141,0.0800455610171,0.0802024515718,0.0802024515718,0.0801710734609,0.0805789889031,0.0804848545703,0.0807358794578,0.0807358794578,0.0806103670141,0.080641745125,0.0809869043454,0.0808927700126,0.0803593421265,0.0804534764594,0.0809241481235,0.0814575760096,0.0815830884533,0.0817086008971,0.0822420287831,0.0821478944503,0.0822734068941,0.082336163116,0.0829637253348,0.0831833721114,0.0830892377786,0.0826813223364,0.0827440785582,0.0828068347801,0.0822734068941,0.0820537601175,0.0820537601175,0.0818654914518,0.0815203322314,0.0810182824563,0.0809555262345,0.0809555262345,0.0807986356797,0.0807986356797,0.0809555262345,0.0805476107922,0.0807986356797,0.0808300137907,0.0808927700126,0.0808927700126,0.0807672575688,0.0804534764594,0.0802338296828,0.0800141829061,0.0799514266843,0.0802024515718,0.0799200485733,0.0798886704624,0.0797317799077,0.079512133131,0.079543511242,0.0800141829061,0.0799514266843,0.0798572923514,0.0798259142405,0.0798572923514,0.0799828047952,0.0800455610171,0.0800455610171,0.0802652077937,0.0804220983484,0.0802965859046,0.0806103670141,0.0805162326812,0.0804534764594,0.0803279640156,0.0797945361295,0.0799514266843,0.0801710734609,0.0802338296828,0.0801710734609,0.080108317239,0.0797631580186,0.0799514266843,0.0805789889031,0.0808927700126,0.0813634416767,0.0813634416767,0.0815830884533,0.0816144665643,0.0816458446752,0.0818027352299,0.0820537601175,0.0823675412269,0.0821165163394,0.0819910038956,0.0821792725613,0.0821165163394,0.0818027352299,0.0820851382284,0.0824616755597,0.0826499442254,0.0827440785582,0.0826185661145,0.0827127004473,0.082869591002,0.0828382128911,0.0832461283333,0.083434396999,0.0830578596677,0.0827127004473,0.0829951034458,0.0830578596677,0.0834657751099,0.0837481781084,0.0837481781084,0.0840305811069,0.0836226656647,0.0835285313318,0.0836226656647,0.0834971532209,0.0829637253348,0.0832775064443,0.0827754566692,0.0821478944503,0.0818341133409,0.081206551122,0.0814261978986,0.0811437949001,0.0811124167892,0.0810810386782,0.0812693073439,0.0807986356797,0.0807672575688,0.0807986356797,0.0809555262345,0.0806103670141,0.0803907202375,0.0803279640156,0.0805476107922,0.0804220983484,0.0801396953499,0.080108317239,0.0802652077937,0.0805162326812,0.0804534764594,0.0810496605673,0.0810810386782,0.0813320635658,0.0811437949001,0.0809241481235,0.0806103670141,0.0802965859046,0.0799514266843,0.0797317799077,0.0793866206873,0.079010083356,0.0787276803575,0.0785080335809,0.0785707898027,0.0787276803575,0.0787904365793,0.078978705245,0.0792297301326,0.079512133131,0.0796376455748,0.0798572923514,0.0798259142405,0.0796062674639,0.0796376455748,0.0792924863544,0.079512133131,0.0794493769092,0.0792924863544,0.0793552425763,0.0799828047952,0.080108317239,0.0803279640156,0.0806103670141,0.0804848545703,0.0811124167892,0.0807986356797,0.0809869043454,0.0812379292329,0.0807358794578,0.0801710734609,0.0798572923514,0.0798259142405,0.080108317239,0.0804534764594,0.080673123236,0.0810810386782,0.0810496605673,0.0808613919016,0.0813948197877,0.0815830884533,0.0815517103424,0.0813320635658,0.0812693073439,0.0811124167892,0.0807358794578,0.0808300137907,0.0807672575688,0.0810182824563,0.0808300137907,0.0807672575688,0.0807672575688,0.0807672575688,0.080641745125,0.0807358794578,0.0809869043454,0.0809241481235,0.0808300137907,0.0807672575688,0.0805162326812,0.0809241481235,0.0813006854548,0.0816772227862,0.0815203322314,0.0814575760096,0.0811124167892,0.0808613919016,0.0813006854548,0.0811437949001,0.0814889541205,0.0811751730111,0.0809555262345,0.0808927700126,0.0813320635658,0.0814575760096,0.0818968695628,0.0819596257846,0.0820537601175,0.0821792725613,0.0820223820065,0.0821478944503,0.0823675412269,0.0823989193379,0.0822106506722,0.0818341133409,0.0814575760096,0.0815203322314,0.081206551122,0.0810182824563,0.0809869043454,0.0810182824563,0.0809555262345,0.0807358794578,0.0807045013469,0.0807045013469,0.0810810386782,0.0810182824563,0.0805162326812,0.0804848545703,0.0804848545703,0.0804220983484,0.0805162326812,0.0807045013469,0.0810182824563,0.0810182824563,0.0805476107922,0.0810496605673,0.081739979008,0.0816772227862,0.081739979008,0.0816458446752,0.0813634416767,0.0813006854548,0.0808613919016,0.0813634416767,0.0814889541205,0.0814261978986,0.0811751730111,0.0816458446752,0.0816772227862,0.0817086008971,0.0819910038956,0.0819910038956,0.0821478944503,0.0820537601175,0.0820537601175,0.0816772227862,0.0814261978986,0.0812379292329,0.0813006854548,0.0816458446752,0.0813634416767,0.0815830884533,0.0819282476737,0.0813948197877,0.0816772227862,0.081771357119,0.0822734068941,0.0822420287831,0.0828382128911,0.0831833721114,0.0834971532209,0.0837481781084,0.0837795562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m <- 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ycorr <- 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altd  <- c(1, 37, 50, 54, 113, 154, 207, 278, 288, 370, 384, 444, 470, 487, 515, 533, 560, 565, 586)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('77-EBS-CLF-GSE101428/EBSdeltaC-FLAG-Rep2-GSM2915141/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) : 1,37,50,54,113,154,207,278,288,370,384,444,470,487,515,533,560,565,586',bty='n')
dev.off()