# R script for Peak Model
#  -- generated by MACS
p <- c(0.0512626807684,0.0555795380963,0.0658320742499,0.0755450032376,0.0847183250594,0.0863371465573,0.0830995035614,0.0895747895532,0.0884955752212,0.0868767537233,0.0901143967192,0.0938916468811,0.0917332182171,0.0890351823872,0.0868767537233,0.0852579322253,0.0857975393913,0.0809410748975,0.0825598963954,0.0847183250594,0.0809410748975,0.0793222533995,0.0782430390676,0.0771638247356,0.0739261817397,0.0733865745737,0.0712281459098,0.0723073602417,0.0674508957479,0.0690697172458,0.0690697172458,0.0723073602417,0.0744657889057,0.0793222533995,0.0874163608893,0.0847183250594,0.0868767537233,0.0852579322253,0.0906540038852,0.0895747895532,0.0944312540471,0.0906540038852,0.0841787178934,0.0793222533995,0.0739261817397,0.0744657889057,0.0701489315778,0.0685301100799,0.062594431254,0.0577379667602,0.0518022879344,0.0496438592705,0.0545003237643,0.0561191452622,0.0566587524282,0.0577379667602,0.0604360025901,0.064213252752,0.063673645586,0.062594431254,0.064752859918,0.065292467084,0.0658320742499,0.06313403842,0.0620548240881,0.06313403842,0.0609756097561,0.0615152169221,0.06313403842,0.0679905029139,0.065292467084,0.0679905029139,0.0685301100799,0.0744657889057,0.0728469674077,0.0766242175696,0.0782430390676,0.0804014677315,0.0847183250594,0.0852579322253,0.0917332182171,0.0890351823872,0.0895747895532,0.0847183250594,0.0890351823872,0.0852579322253,0.0836391107274,0.0798618605655,0.0755450032376,0.0733865745737,0.0701489315778,0.0717677530758,0.0706885387438,0.0712281459098,0.0701489315778,0.0701489315778,0.0712281459098,0.0733865745737,0.0744657889057,0.0733865745737,0.0712281459098,0.0723073602417,0.0690697172458,0.0696093244118,0.0690697172458,0.0696093244118,0.0723073602417,0.0690697172458,0.0685301100799,0.0701489315778,0.0750053960717,0.0739261817397,0.0739261817397,0.0701489315778,0.0674508957479,0.064213252752,0.0615152169221,0.0582775739262,0.0561191452622,0.0539607165983,0.0550399309303,0.0577379667602,0.062594431254,0.0685301100799,0.0712281459098,0.0733865745737,0.0717677530758,0.0728469674077,0.0798618605655,0.0809410748975,0.0750053960717,0.0771638247356,0.0739261817397,0.0723073602417,0.0706885387438,0.0701489315778,0.0723073602417,0.0739261817397,0.0685301100799,0.0717677530758,0.0717677530758,0.0701489315778,0.0706885387438,0.0696093244118,0.0733865745737,0.0755450032376,0.0739261817397,0.0744657889057,0.0739261817397,0.0723073602417,0.0750053960717,0.0771638247356,0.0787826462335,0.0798618605655,0.0793222533995,0.0804014677315,0.0825598963954,0.0863371465573,0.0868767537233,0.0852579322253,0.0890351823872,0.0847183250594,0.0841787178934,0.0868767537233,0.0884955752212,0.0868767537233,0.0874163608893,0.0825598963954,0.0814806820635,0.0825598963954,0.0766242175696,0.0766242175696,0.0750053960717,0.0712281459098,0.064752859918,0.0615152169221,0.0571983595942,0.0609756097561,0.0620548240881,0.0571983595942,0.0571983595942,0.0593567882581,0.0588171810922,0.0598963954241,0.0615152169221,0.064752859918,0.065292467084,0.062594431254,0.063673645586,0.0685301100799,0.0696093244118,0.0674508957479,0.0674508957479,0.0679905029139,0.0696093244118,0.0701489315778,0.0755450032376,0.0755450032376,0.0760846104036,0.0766242175696,0.0787826462335,0.0814806820635,0.0814806820635,0.0809410748975,0.0836391107274,0.0841787178934,0.0814806820635,0.0809410748975,0.0814806820635,0.0809410748975,0.0777034319016,0.0755450032376,0.0766242175696,0.0766242175696,0.0717677530758,0.0685301100799,0.0658320742499,0.06313403842,0.0598963954241,0.0577379667602,0.0577379667602,0.0582775739262,0.0577379667602,0.0609756097561,0.064752859918,0.0712281459098,0.0723073602417,0.0771638247356,0.0793222533995,0.0793222533995,0.0793222533995,0.0739261817397,0.0733865745737,0.0679905029139,0.064213252752,0.0588171810922,0.0604360025901,0.0588171810922,0.0588171810922,0.0615152169221,0.0604360025901,0.0615152169221,0.0658320742499,0.0674508957479,0.0685301100799,0.0685301100799,0.0658320742499,0.0674508957479,0.065292467084,0.062594431254,0.064213252752,0.0663716814159,0.064213252752,0.0615152169221,0.0620548240881,0.0620548240881,0.065292467084,0.062594431254,0.064752859918,0.0663716814159,0.0669112885819,0.064213252752,0.0658320742499,0.0658320742499,0.0696093244118,0.0701489315778,0.0674508957479,0.0701489315778,0.0685301100799,0.0706885387438,0.0712281459098,0.0760846104036,0.0717677530758,0.0771638247356,0.0750053960717,0.0723073602417,0.0728469674077,0.0690697172458,0.0728469674077,0.0739261817397,0.0733865745737,0.0723073602417,0.0733865745737,0.0674508957479,0.0679905029139,0.0712281459098,0.0728469674077,0.0739261817397,0.0696093244118,0.0696093244118,0.0685301100799,0.0674508957479,0.0679905029139,0.0696093244118,0.0663716814159,0.0620548240881,0.063673645586,0.064213252752,0.0658320742499,0.0582775739262,0.0598963954241,0.0598963954241,0.0577379667602,0.0593567882581,0.0582775739262,0.065292467084,0.062594431254,0.064752859918,0.06313403842,0.0669112885819,0.0696093244118,0.0739261817397,0.0750053960717,0.0766242175696,0.08040146773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m <- 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ycorr <- 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altd  <- c(36, 88, 183, 238, 391, 419, 461, 522, 584)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('48-PIF1-PIF4-GSE43286/PIF4-peaks-1-GSM1059963/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) : 36,88,183,238,391,419,461,522,584',bty='n')
dev.off()