# R script for Peak Model
#  -- generated by MACS
p <- c(0.0482451787186,0.056415501173,0.0644132111813,0.0723533837074,0.0804086311977,0.0804661686798,0.0804373999387,0.0805812436439,0.0804949374208,0.0807538560901,0.0808113935722,0.0807250873491,0.0808113935722,0.0810990809826,0.0815018433571,0.0812141559467,0.0809264685363,0.0805812436439,0.0804949374208,0.0804086311977,0.0804661686798,0.0803510937156,0.0803223249746,0.0800346375642,0.0794880314845,0.0796031064487,0.0795455689666,0.0796894126718,0.0797181814128,0.0796606439307,0.0797181814128,0.0799483313411,0.079862025118,0.0797757188949,0.0796606439307,0.0796606439307,0.0797469501538,0.0800921750463,0.0802360187515,0.0802935562335,0.0801497125284,0.0796606439307,0.0798044876359,0.0799483313411,0.0803223249746,0.0801784812694,0.0804086311977,0.0802647874925,0.079890793859,0.0800058688232,0.0799195626001,0.0801784812694,0.0800921750463,0.0801497125284,0.079890793859,0.079833256377,0.0795455689666,0.0791715753331,0.0792003440741,0.07908526911,0.0788838879227,0.0785962005124,0.078279744361,0.0781071319147,0.0781071319147,0.0780495944327,0.0779632882096,0.0781071319147,0.0780495944327,0.0780783631737,0.0780783631737,0.0782222068789,0.0783660505841,0.078308513102,0.0783948193251,0.0781934381379,0.0785386630303,0.0785386630303,0.0786249692534,0.0785386630303,0.0787112754765,0.079056500369,0.0792291128152,0.0794880314845,0.0797469501538,0.0802935562335,0.0804949374208,0.0806100123849,0.0808401623132,0.0810415435005,0.0809552372774,0.0808113935722,0.0807538560901,0.080638781126,0.0803510937156,0.0801497125284,0.0800921750463,0.0802072500104,0.0802072500104,0.0797469501538,0.079833256377,0.0796894126718,0.0796031064487,0.0795743377076,0.0796606439307,0.0799771000821,0.0799771000821,0.0799195626001,0.0798044876359,0.0800634063052,0.0801784812694,0.0803510937156,0.0805812436439,0.0807826248312,0.0808401623132,0.0807826248312,0.0806963186081,0.0808689310543,0.0810703122415,0.0812141559467,0.081473074616,0.0817032245443,0.0817319932854,0.0818758369906,0.0819621432137,0.0821059869189,0.0824224430703,0.0823073681061,0.0825087492934,0.0826238242575,0.0822785993651,0.0818182995085,0.0820196806957,0.0818758369906,0.0817607620264,0.0819046057316,0.0818182995085,0.0819621432137,0.0816744558033,0.0818758369906,0.082192293142,0.0827101304806,0.0828827429268,0.0831128928551,0.0831704303372,0.083026586632,0.0829115116679,0.0828252054448,0.0832567365603,0.0832279678193,0.0832567365603,0.0833142740424,0.0833430427834,0.0833142740424,0.0833718115245,0.0833430427834,0.0831704303372,0.0830553553731,0.0826813617396,0.0823936743292,0.0823361368471,0.0823361368471,0.0817607620264,0.0813004621698,0.0813867683929,0.0810703122415,0.0812429246878,0.0813579996519,0.0812716934288,0.0811853872057,0.0811566184646,0.0808113935722,0.0808976997953,0.0810703122415,0.0810127747595,0.0813867683929,0.0812716934288,0.0810127747595,0.0811566184646,0.0812716934288,0.0811566184646,0.0810703122415,0.0811566184646,0.0810990809826,0.0810127747595,0.0805524749029,0.0805237061618,0.0809264685363,0.0806963186081,0.080638781126,0.0808113935722,0.0810990809826,0.0809840060184,0.0810703122415,0.0812141559467,0.0813579996519,0.0813579996519,0.0810703122415,0.0810990809826,0.0809552372774,0.0807538560901,0.0806963186081,0.080667549867,0.0807538560901,0.080638781126,0.0810127747595,0.0809840060184,0.0810127747595,0.0810415435005,0.0811853872057,0.0812141559467,0.0811566184646,0.0812716934288,0.0811278497236,0.0809840060184,0.0806100123849,0.0808976997953,0.0810703122415,0.0811566184646,0.0812716934288,0.0813579996519,0.0815018433571,0.0817895307674,0.082249830624,0.082249830624,0.082192293142,0.0821059869189,0.0820196806957,0.082221061883,0.0823649055882,0.082192293142,0.0819333744726,0.0818470682495,0.0816456870623,0.0818182995085,0.0820772181778,0.082249830624,0.0823361368471,0.0826238242575,0.0825375180344,0.0826238242575,0.08296904915,0.0825950555165,0.0828252054448,0.0828539741858,0.0828539741858,0.0826525929986,0.0827676679627,0.0828252054448,0.0828827429268,0.0831416615962,0.0829115116679,0.0832855053014,0.0832567365603,0.0832567365603,0.0830553553731,0.0830841241141,0.0827676679627,0.0822785993651,0.0820772181778,0.0819621432137,0.0817895307674,0.0815018433571,0.0812429246878,0.0808976997953,0.0810990809826,0.0812429246878,0.0815881495802,0.0816456870623,0.0818182995085,0.0817895307674,0.0821347556599,0.0823073681061,0.082221061883,0.0825375180344,0.0826238242575,0.0825662867754,0.0822785993651,0.0823073681061,0.0822785993651,0.0825087492934,0.0825087492934,0.0830841241141,0.0834293490065,0.08380334264,0.0837458051579,0.0838321113811,0.0838896488631,0.0841197987914,0.0844362549428,0.0846376361301,0.0848965547994,0.0846664048711,0.084608867389,0.0845225611659,0.0846376361301,0.0847814798353,0.0850691672456,0.0848102485763,0.0846376361301,0.0844362549428,0.0839471863452,0.0836594989348,0.0836019614528,0.0837458051579,0.0836594989348,0.0835731927117,0.0835731927117,0.0838896488631,0.0840334925683,0.0839759550862,0.0840910300504,0.0842636424966,0.0841773362735,0.08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m <- 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ycorr <- 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altd  <- c(0, 31, 45, 65, 95, 111, 130, 210, 550)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('33-SEP3-AP1-24581456/SEP3-ChIP-seq-8d-biological-reps-1-and-2-GSM1142625/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) : 0,31,45,65,95,111,130,210,550',bty='n')
dev.off()