# R script for Peak Model
#  -- generated by MACS
p <- c(0.0486367775457,0.0568857464246,0.0650811505705,0.0729551663185,0.0811505704644,0.0811505704644,0.0813648293963,0.0804542289357,0.0802935347367,0.0801864052708,0.0801328405378,0.0799721463389,0.0797578874069,0.079543628475,0.0793293695431,0.0784187690824,0.0787401574803,0.0792222400771,0.0790079811452,0.0790615458782,0.0792222400771,0.0793829342761,0.0791686753442,0.0797578874069,0.0799185816059,0.0805613584016,0.0804542289357,0.0804006642027,0.0810434409984,0.0809898762655,0.0808291820665,0.0805077936686,0.0807220526006,0.0806684878676,0.0808827467995,0.0807220526006,0.0807220526006,0.0810434409984,0.0803470994697,0.0804006642027,0.0806149231346,0.0806684878676,0.0805613584016,0.0806149231346,0.0801864052708,0.0799721463389,0.079704322674,0.0791686753442,0.079543628475,0.0794364990091,0.0791151106112,0.0791686753442,0.0793293695431,0.0787401574803,0.0787401574803,0.0788472869463,0.0791686753442,0.0791686753442,0.0789544164122,0.0789544164122,0.079490063742,0.0793293695431,0.079597193208,0.0799185816059,0.0801328405378,0.0804542289357,0.0800792758048,0.0805613584016,0.0808827467995,0.0813648293963,0.0808827467995,0.0808291820665,0.0807756173335,0.0807220526006,0.0806684878676,0.0804542289357,0.0807756173335,0.0807756173335,0.0802399700037,0.0800257110718,0.0803470994697,0.0807220526006,0.0805613584016,0.0808291820665,0.0808291820665,0.0804006642027,0.0808291820665,0.0805077936686,0.0804006642027,0.0806684878676,0.0805077936686,0.0801328405378,0.0804006642027,0.0804006642027,0.0803470994697,0.0807220526006,0.0805077936686,0.0806149231346,0.0805613584016,0.0802399700037,0.0801864052708,0.0802935347367,0.0800257110718,0.0798114521399,0.079597193208,0.0798114521399,0.079650757941,0.079597193208,0.0797578874069,0.079650757941,0.079543628475,0.0794364990091,0.079490063742,0.0798114521399,0.0798650168729,0.079597193208,0.079490063742,0.0793293695431,0.0798114521399,0.0800257110718,0.0805613584016,0.0810434409984,0.0815255235953,0.0810434409984,0.0816326530612,0.0820076061921,0.082114735658,0.0824896887889,0.0824896887889,0.0823825593229,0.082221865124,0.0820611709251,0.0815790883282,0.08232899459,0.08232899459,0.0824361240559,0.0823825593229,0.082114735658,0.0816326530612,0.0819004767261,0.0819540414591,0.0820076061921,0.082114735658,0.0814719588623,0.0812576999304,0.0809898762655,0.0813648293963,0.0815790883282,0.0819004767261,0.082168300391,0.08232899459,0.0824361240559,0.0820611709251,0.082168300391,0.082168300391,0.082114735658,0.0819540414591,0.0817397825272,0.0818469119931,0.0813112646633,0.0812576999304,0.0809898762655,0.0815790883282,0.0814183941293,0.0809898762655,0.0809363115325,0.0807756173335,0.0811505704644,0.0804542289357,0.0805613584016,0.0804542289357,0.0799185816059,0.0791686753442,0.0794364990091,0.0793829342761,0.0789008516793,0.0789008516793,0.0789008516793,0.0793829342761,0.079597193208,0.079597193208,0.0801864052708,0.0799721463389,0.0799721463389,0.0804542289357,0.0808827467995,0.0808827467995,0.0805077936686,0.0805077936686,0.0806149231346,0.0805077936686,0.0808827467995,0.0812041351974,0.0812576999304,0.0808827467995,0.0808291820665,0.0810434409984,0.0815255235953,0.0820611709251,0.0820076061921,0.0819004767261,0.0814183941293,0.0816862177942,0.0816862177942,0.0818469119931,0.0818469119931,0.0818469119931,0.0814183941293,0.0808291820665,0.0809363115325,0.0809363115325,0.0806684878676,0.0812576999304,0.0814183941293,0.0810434409984,0.0813648293963,0.0815790883282,0.0813648293963,0.0814719588623,0.0808291820665,0.0813112646633,0.0819004767261,0.0810970057314,0.0807756173335,0.0812576999304,0.0809898762655,0.0807756173335,0.0812041351974,0.0814183941293,0.082168300391,0.082168300391,0.0819540414591,0.082275429857,0.0827039477208,0.0827039477208,0.0826503829878,0.0824361240559,0.0824896887889,0.0827575124538,0.082168300391,0.0816862177942,0.0818469119931,0.082168300391,0.082221865124,0.082221865124,0.082221865124,0.0824896887889,0.0826503829878,0.0826503829878,0.0829717713857,0.0832395950506,0.0835074187155,0.0831324655847,0.0828110771868,0.0824361240559,0.0828110771868,0.0825432535219,0.0825968182549,0.082221865124,0.0819540414591,0.0817397825272,0.0810434409984,0.0811505704644,0.0807220526006,0.0805613584016,0.0800792758048,0.0806149231346,0.0801864052708,0.0805077936686,0.0802399700037,0.0800257110718,0.0802935347367,0.0800792758048,0.0801328405378,0.0806149231346,0.0809898762655,0.0807756173335,0.0809363115325,0.0804542289357,0.0809363115325,0.0814183941293,0.0812576999304,0.0812041351974,0.0814183941293,0.0809363115325,0.0806149231346,0.0806149231346,0.0808291820665,0.0807220526006,0.0807220526006,0.0805613584016,0.0810970057314,0.0817397825272,0.0820076061921,0.0825432535219,0.0830253361187,0.0830253361187,0.0832395950506,0.0835609834485,0.0837752423804,0.0843644544432,0.0844715839092,0.0839895013123,0.0840430660453,0.0845251486421,0.0845787133751,0.0851679254379,0.0852214901709,0.0855428785688,0.0852214901709,0.084900101773,0.0846858428411,0.0851679254379,0.0853286196368,0.08581070223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m <- 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ycorr <- 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altd  <- c(0, 40, 93, 99, 108, 117, 130, 132, 158, 195, 263, 288, 410, 459, 497, 522, 544, 568)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('80-APR1-APR10-APR12-APR14-GSE94486/ARR14ypet_p6BA-GSM2476327/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) : 0,40,93,99,108,117,130,132,158,195,263,288,410,459,497,522,544,568',bty='n')
dev.off()