# R script for Peak Model
#  -- generated by MACS
p <- c(0.0476852589813,0.0555475377066,0.0634098164319,0.0712720951573,0.079269001943,0.0793497787792,0.0793767043912,0.0794844068395,0.0794305556154,0.079295927555,0.0793497787792,0.0793767043912,0.0796190348999,0.0797805885723,0.0798075141844,0.0797536629603,0.0799959934689,0.0797805885723,0.0797805885723,0.0798344397965,0.0799690678569,0.0801844727534,0.0801575471414,0.0801036959172,0.0801036959172,0.0801844727534,0.0801575471414,0.0802383239776,0.0802921752017,0.0802383239776,0.0802113983655,0.0802383239776,0.0802383239776,0.0801575471414,0.0802113983655,0.0804268032621,0.08039987765,0.0805345057104,0.0805883569345,0.0809114642794,0.0809383898915,0.081126869176,0.0812884228484,0.0815307533571,0.0815307533571,0.0815576789692,0.0817730838657,0.0818269350899,0.0819077119261,0.0816384558054,0.0817461582537,0.0814769021329,0.0813153484605,0.0811537947881,0.0809922411156,0.0810191667277,0.0808037618311,0.080776836219,0.0806152825466,0.0805883569345,0.0803460264259,0.0802113983655,0.0802921752017,0.0804268032621,0.0806422081587,0.0804268032621,0.0803460264259,0.0803460264259,0.0803460264259,0.0804537288742,0.0806152825466,0.080749910607,0.0805883569345,0.0805075800983,0.0804268032621,0.0804268032621,0.0805345057104,0.0803191008138,0.0802921752017,0.0802921752017,0.0800498446931,0.080022919081,0.0800498446931,0.0800767703051,0.0801575471414,0.0802652495897,0.0803729520379,0.0804806544862,0.08039987765,0.0801844727534,0.0802652495897,0.08039987765,0.0806691337707,0.0809114642794,0.0809383898915,0.081126869176,0.0810999435639,0.0811807204001,0.0813422740726,0.0815846045812,0.0816923070295,0.0815846045812,0.0812614972364,0.0810730179518,0.0810191667277,0.0808037618311,0.0808845386673,0.0811537947881,0.0812076460122,0.0811537947881,0.0811537947881,0.0813153484605,0.0815307533571,0.0816923070295,0.0818000094778,0.0820154143744,0.0819615631503,0.081880786314,0.0820154143744,0.0821769680468,0.0822577448831,0.0822846704951,0.0823923729434,0.0823385217193,0.0823654473313,0.0824731497796,0.0823923729434,0.0823385217193,0.0822038936589,0.0821231168227,0.0819077119261,0.0817461582537,0.0815576789692,0.0813691996846,0.0810999435639,0.0805614313225,0.0805614313225,0.0803460264259,0.0803729520379,0.0801844727534,0.0801844727534,0.0801844727534,0.0801844727534,0.0801036959172,0.0799421422448,0.0800767703051,0.0799959934689,0.0801036959172,0.0799152166327,0.0799421422448,0.0798882910206,0.0797536629603,0.0797536629603,0.079645960512,0.0799152166327,0.0798613654086,0.0797805885723,0.079672886124,0.0797267373482,0.0797536629603,0.0797267373482,0.0796190348999,0.0794305556154,0.0794844068395,0.0793767043912,0.0794844068395,0.0793767043912,0.079269001943,0.0790266714343,0.0788920433739,0.0791612994947,0.0793497787792,0.079269001943,0.0792151507188,0.0791343738826,0.0788381921498,0.0788920433739,0.0788112665377,0.0789458945981,0.0789458945981,0.0785958616411,0.0784881591928,0.0785150848049,0.0787035640894,0.0788651177619,0.0791343738826,0.0793497787792,0.0797267373482,0.0799690678569,0.0799959934689,0.0803191008138,0.0805883569345,0.0809922411156,0.0811807204001,0.0813422740726,0.0814499765209,0.0816115301933,0.0815846045812,0.0814769021329,0.0816653814175,0.0816115301933,0.0815846045812,0.0814230509088,0.0813153484605,0.0811807204001,0.081126869176,0.0811537947881,0.0810999435639,0.0813691996846,0.0813691996846,0.0813422740726,0.0812884228484,0.081126869176,0.0810191667277,0.0809922411156,0.0809922411156,0.080776836219,0.0808037618311,0.0804806544862,0.0803729520379,0.0803460264259,0.0801575471414,0.0802652495897,0.0804537288742,0.0805075800983,0.0805075800983,0.08039987765,0.0803460264259,0.0804537288742,0.0803729520379,0.0804268032621,0.0805614313225,0.0804268032621,0.080022919081,0.0798613654086,0.0798075141844,0.0797536629603,0.0798075141844,0.0797805885723,0.0800498446931,0.0800498446931,0.0801306215293,0.0802921752017,0.0807229849949,0.0806960593828,0.080776836219,0.0809383898915,0.0809653155036,0.0808306874432,0.0806691337707,0.0806152825466,0.0804268032621,0.0803729520379,0.0803191008138,0.0804268032621,0.0803729520379,0.0804806544862,0.0803191008138,0.0805345057104,0.0805883569345,0.0805614313225,0.0806422081587,0.0806960593828,0.0806422081587,0.080776836219,0.0806691337707,0.0805345057104,0.080749910607,0.0806422081587,0.0805883569345,0.0806152825466,0.0804806544862,0.0803460264259,0.0802921752017,0.0800767703051,0.0801306215293,0.0801036959172,0.0798075141844,0.0795921092878,0.0795651836758,0.0793228531671,0.0794305556154,0.0795651836758,0.0798075141844,0.080022919081,0.0802113983655,0.0805614313225,0.0809383898915,0.0813691996846,0.0816115301933,0.0818269350899,0.0820692655985,0.0821769680468,0.0820423399865,0.0820961912106,0.0822577448831,0.0820154143744,0.0820154143744,0.081853860702,0.0818000094778,0.0819884887623,0.0820154143744,0.082230819271,0.0822846704951,0.0822038936589,0.0821231168227,0.0823654473313,0.0824462241676,0.0825808522279,0.0827962571245,0.0828770339607,0.082957810797,0.082984736409,0.0831732156935,0.0833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m <- 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ycorr <- 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altd  <- c(34, 96, 198, 247, 360, 379, 414, 509, 544, 591)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('08-CMT-GSE39097/CMT3_ChIPseq-GSM956128/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) : 34,96,198,247,360,379,414,509,544,591',bty='n')
dev.off()