# R script for Peak Model
#  -- generated by MACS
p <- c(0.0473442094105,0.0555389941876,0.0639502449777,0.0719904111741,0.0798450350737,0.0795357979123,0.0791028658863,0.0795667216284,0.0798141113575,0.079906882506,0.0800924248028,0.0795357979123,0.079041018454,0.0787317812926,0.0787008575765,0.0786699338604,0.0787317812926,0.0785153152797,0.0783297729828,0.0782060781183,0.0780205358214,0.0780514595376,0.0780205358214,0.0779896121053,0.0781751544021,0.0784843915635,0.0787008575765,0.0786390101442,0.0785153152797,0.0787936287249,0.0792884081832,0.0796285690607,0.0798141113575,0.0797522639253,0.0795667216284,0.0793502556154,0.07947395048,0.0793502556154,0.0796594927768,0.0796285690607,0.0789791710218,0.0787008575765,0.0780205358214,0.078144230686,0.0780205358214,0.0779896121053,0.0777422223762,0.0774020614986,0.0767835871758,0.0767526634597,0.076814510892,0.0769072820404,0.0774329852148,0.0768763583242,0.0767217397435,0.0763506551499,0.076381578866,0.0766289685951,0.0770619006211,0.0771855954856,0.0768763583242,0.076598044879,0.0765671211628,0.0773402140663,0.0775876037955,0.0781751544021,0.0778349935246,0.0775257563632,0.0768454346081,0.0765361974467,0.0766908160274,0.0770000531888,0.0765361974467,0.0758249519755,0.0757631045432,0.0752683250849,0.0754847910979,0.0756394096786,0.0757940282593,0.0757631045432,0.0763197314337,0.0762888077176,0.076598044879,0.0772165192018,0.0775566800793,0.0773402140663,0.0778659172407,0.0780205358214,0.0780205358214,0.0783297729828,0.078360696699,0.0783916204151,0.0786080864281,0.0783916204151,0.0780205358214,0.0786080864281,0.078360696699,0.078360696699,0.0789482473056,0.0789482473056,0.0788245524411,0.078360696699,0.0784843915635,0.0788863998733,0.0786390101442,0.0784843915635,0.0781133069698,0.0780514595376,0.0777422223762,0.0776494512277,0.0771237480534,0.0775257563632,0.0773711377825,0.0767835871758,0.0770000531888,0.0771237480534,0.0776803749439,0.0778040698084,0.077927764673,0.0780514595376,0.0785462389958,0.0787936287249,0.0791028658863,0.0791956370347,0.0798141113575,0.0800924248028,0.0799378062221,0.0799687299382,0.0798450350737,0.0795048741961,0.0794121030477,0.0794121030477,0.0788245524411,0.0791647133186,0.0788863998733,0.0788554761572,0.0791028658863,0.0791647133186,0.0787627050088,0.0789482473056,0.0793502556154,0.0791956370347,0.0795667216284,0.0796594927768,0.0798450350737,0.0795976453446,0.0793502556154,0.0795667216284,0.0804325856803,0.0807418228417,0.0804016619642,0.0802470433835,0.0799687299382,0.0799378062221,0.0793502556154,0.0793502556154,0.0792265607509,0.0785771627119,0.0780514595376,0.0775566800793,0.0778659172407,0.078144230686,0.0780514595376,0.078144230686,0.0784225441312,0.0781133069698,0.0780823832537,0.0783297729828,0.0783297729828,0.0785153152797,0.0780823832537,0.0780514595376,0.0783297729828,0.0782679255505,0.0784534678474,0.0791028658863,0.079257484467,0.0792884081832,0.0802470433835,0.0804325856803,0.0807108991256,0.0808655177063,0.0809582888547,0.0809892125709,0.080803670274,0.0807727465579,0.0807727465579,0.0807108991256,0.079257484467,0.0790719421702,0.0787627050088,0.0782060781183,0.0778349935246,0.07771129866,0.0775876037955,0.0771546717695,0.0772474429179,0.0770000531888,0.0774639089309,0.0771546717695,0.0767217397435,0.076598044879,0.076381578866,0.0759795705562,0.07594864684,0.075732180827,0.0753920199495,0.0755466385302,0.0758558756916,0.0762269602853,0.0766908160274,0.0767526634597,0.0770309769049,0.0771237480534,0.0769072820404,0.0772474429179,0.0771546717695,0.0770309769049,0.0768454346081,0.0764125025821,0.0761341891369,0.0764743500144,0.076598044879,0.0767526634597,0.0774639089309,0.0774020614986,0.0772474429179,0.0775566800793,0.0777422223762,0.0778659172407,0.0782988492667,0.077927764673,0.0777731460923,0.0779896121053,0.0773711377825,0.0772474429179,0.0776494512277,0.0780205358214,0.0777731460923,0.0782988492667,0.0779896121053,0.0787936287249,0.079041018454,0.0789482473056,0.0792884081832,0.0798450350737,0.0797831876414,0.0795976453446,0.0803398145319,0.0801233485189,0.0809273651386,0.0806490516933,0.0810819837193,0.0813293734484,0.0818241529066,0.0817313817582,0.0819787714873,0.0821643137842,0.0815767631775,0.0822261612165,0.0820406189196,0.0822880086487,0.082133390068,0.0822570849326,0.0819787714873,0.0817313817582,0.0812984497323,0.0813912208807,0.0817004580421,0.0808964414224,0.0805562805449,0.0800615010867,0.079690416493,0.0792884081832,0.0789791710218,0.0790719421702,0.0792884081832,0.0785462389958,0.0782988492667,0.0784225441312,0.0785771627119,0.0785771627119,0.0786699338604,0.0784225441312,0.0786080864281,0.0788245524411,0.0785771627119,0.0787008575765,0.0786699338604,0.0785462389958,0.0783297729828,0.0784843915635,0.0785153152797,0.079041018454,0.0793502556154,0.0791647133186,0.0793502556154,0.0797213402091,0.0800924248028,0.0808964414224,0.0813293734484,0.0815149157452,0.0812984497323,0.0815767631775,0.0811129074354,0.0812366023,0.0811747548677,0.0813293734484,0.0814839920291,0.0813912208807,0.0810510600031,0.0812984497323,0.0818860003389,0.0820096952035,0.0825353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m <- 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ycorr <- 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altd  <- c(1, 47, 54, 99, 594)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('06-PIF3-GSE39215/P3M-ChIP-2-GSM958270/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) : 1,47,54,99,594',bty='n')
dev.off()