# R script for Peak Model
#  -- generated by MACS
p <- c(0.0484456804527,0.0564786950423,0.064456688984,0.0723521519538,0.0804676975152,0.0807428007546,0.0810179039939,0.0813205175572,0.0812104762615,0.0812379865854,0.0812930072333,0.0811554556136,0.0814855795008,0.0816781517684,0.0817331724163,0.0816231311205,0.0816781517684,0.0817056620923,0.081870724036,0.0818982343599,0.0817331724163,0.0821733375993,0.0817056620923,0.0816506414445,0.0814580691769,0.0813755382051,0.081403048529,0.0812654969094,0.0811279452897,0.0808803523742,0.0807978214024,0.0804952078391,0.0807152904306,0.0806877801067,0.0807978214024,0.0808803523742,0.0807703110785,0.0806327594588,0.0803576562194,0.0804126768673,0.0804126768673,0.0804126768673,0.0801650839519,0.0803851665434,0.0803026355716,0.0801650839519,0.0801650839519,0.0803301458955,0.0803851665434,0.0803301458955,0.0806052491349,0.0806327594588,0.0808528420503,0.0807152904306,0.0806602697827,0.0806327594588,0.0805227181631,0.0803576562194,0.0801650839519,0.0801650839519,0.0799725116843,0.0800000220083,0.0799450013604,0.0797799394168,0.079697408445,0.0796148774731,0.0796423877971,0.0796423877971,0.0798074497407,0.0795598568253,0.0793672845577,0.0791472019662,0.0790646709944,0.0790921813183,0.0793672845577,0.0793397742338,0.0790096503465,0.0790371606705,0.0790646709944,0.0795323465013,0.0796148774731,0.0797799394168,0.079697408445,0.0794498155295,0.0794773258535,0.079697408445,0.0795048361774,0.0793397742338,0.0791747122902,0.0789546296987,0.078789567755,0.0786245058114,0.0786795264593,0.0788445884029,0.0785419748396,0.0784319335439,0.0786795264593,0.078789567755,0.0787070367832,0.078817078079,0.0793397742338,0.0795323465013,0.079669898121,0.0800275323322,0.0801650839519,0.0804952078391,0.0808803523742,0.0809078626982,0.0812930072333,0.0815681104727,0.0812104762615,0.0811554556136,0.081430558853,0.0811004349657,0.0816231311205,0.0817056620923,0.0816506414445,0.0821183169514,0.0821458272753,0.0820908066275,0.0823934201908,0.0823659098668,0.0817881930642,0.0822283582471,0.0816231311205,0.0811829659375,0.0810179039939,0.0807978214024,0.0808528420503,0.0808803523742,0.0807428007546,0.0807152904306,0.0812930072333,0.080962883346,0.0812104762615,0.0812654969094,0.0813205175572,0.081430558853,0.0813480278812,0.0807978214024,0.0804676975152,0.0804401871912,0.0803026355716,0.0803026355716,0.080110063304,0.0802201045998,0.0803576562194,0.0802751252476,0.080550228487,0.0808528420503,0.0812654969094,0.0811829659375,0.0811279452897,0.081430558853,0.0810179039939,0.0808803523742,0.0804676975152,0.0800825529801,0.0795048361774,0.0793672845577,0.0790646709944,0.0788996090508,0.0788996090508,0.0785419748396,0.0788720987268,0.0794223052056,0.0798899807125,0.0803026355716,0.0805227181631,0.0804401871912,0.080550228487,0.0811829659375,0.0812930072333,0.0817331724163,0.0819257446838,0.081403048529,0.0811554556136,0.0812379865854,0.0814580691769,0.0818157033881,0.081843213712,0.0817606827402,0.0817056620923,0.0812930072333,0.081403048529,0.0817606827402,0.0819807653317,0.0818982343599,0.081870724036,0.081843213712,0.0821183169514,0.082310889219,0.082310889219,0.0825309718104,0.0825309718104,0.0825034614865,0.0825584821344,0.0822283582471,0.0819532550078,0.0816506414445,0.0815130898248,0.0810179039939,0.0810454143179,0.080962883346,0.0809078626982,0.0807428007546,0.0804952078391,0.0806877801067,0.0810179039939,0.0811829659375,0.0811554556136,0.0812104762615,0.0811279452897,0.0807703110785,0.0808528420503,0.080962883346,0.0806602697827,0.0806877801067,0.0804952078391,0.0803301458955,0.0797524290928,0.079669898121,0.0794223052056,0.0798624703886,0.0799174910364,0.0797249187689,0.0799725116843,0.0799174910364,0.0799174910364,0.0798624703886,0.0801650839519,0.0803851665434,0.0806052491349,0.0806327594588,0.0804952078391,0.0805227181631,0.0805777388109,0.0808803523742,0.0811004349657,0.0814855795008,0.081870724036,0.0817056620923,0.0819257446838,0.0820357859796,0.0821458272753,0.0823383995429,0.0825859924583,0.0824209305147,0.0823659098668,0.082310889219,0.0821458272753,0.0823934201908,0.0822283582471,0.0819807653317,0.0819257446838,0.0813205175572,0.0808528420503,0.0806052491349,0.0802476149237,0.0803301458955,0.0801650839519,0.0799450013604,0.0801375736279,0.0800825529801,0.0799725116843,0.0806052491349,0.0808803523742,0.0807703110785,0.0807703110785,0.0807152904306,0.0808803523742,0.0809078626982,0.0809078626982,0.0810179039939,0.081403048529,0.0813205175572,0.0813480278812,0.081403048529,0.0817056620923,0.0817331724163,0.081870724036,0.0821733375993,0.0821458272753,0.0822008479232,0.0819532550078,0.0822558685711,0.082310889219,0.0825034614865,0.082723544078,0.0829161163456,0.0828060750498,0.082723544078,0.0826960337541,0.0828335853738,0.0830536679652,0.0829436266695,0.0828610956977,0.0830261576413,0.0829436266695,0.0825859924583,0.0824759511626,0.0823659098668,0.082283378895,0.0821733375993,0.0820908066275,0.0819807653317,0.0822008479232,0.0824484408386,0.0824209305147,0.0831361989371,0.0835488537961,0.0838514673594,0.0842916325424,0.0845942461057,0.08445669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m <- 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ycorr <- 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altd  <- c(0, 45, 69, 85, 116, 135, 293, 471, 518, 560, 582)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('06-PIF3-GSE39215/P3M-ChIP-3-GSM958271/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) : 0,45,69,85,116,135,293,471,518,560,582',bty='n')
dev.off()