# R script for Peak Model
#  -- generated by MACS
p <- c(0.0376330132364,0.0471494073882,0.0562332381694,0.0653170689506,0.0713729561381,0.0748334631023,0.0744008997318,0.076996279955,0.076996279955,0.0800242235487,0.0813219136604,0.0813219136604,0.0778614066961,0.0761311532139,0.0756985898434,0.0739683363613,0.0739683363613,0.076996279955,0.0761311532139,0.0726706462497,0.0735357729907,0.0726706462497,0.0718055195086,0.0700752660265,0.0713729561381,0.0744008997318,0.0735357729907,0.0696427026559,0.0735357729907,0.0752660264729,0.0735357729907,0.0718055195086,0.0752660264729,0.0765637165845,0.076996279955,0.0722380828791,0.0735357729907,0.0756985898434,0.0709403927675,0.0713729561381,0.0718055195086,0.0709403927675,0.070507829397,0.0722380828791,0.0748334631023,0.0744008997318,0.0761311532139,0.0761311532139,0.0761311532139,0.0731032096202,0.0718055195086,0.0718055195086,0.0744008997318,0.0735357729907,0.0739683363613,0.0778614066961,0.0756985898434,0.0726706462497,0.0748334631023,0.0795916601782,0.0804567869193,0.0804567869193,0.0778614066961,0.0782939700666,0.0765637165845,0.0765637165845,0.0765637165845,0.0795916601782,0.0813219136604,0.0804567869193,0.0795916601782,0.0804567869193,0.0800242235487,0.0804567869193,0.0808893502898,0.0782939700666,0.0787265334371,0.0791590968077,0.0774288433255,0.0761311532139,0.0761311532139,0.0774288433255,0.0778614066961,0.0756985898434,0.0718055195086,0.0739683363613,0.0739683363613,0.0731032096202,0.0748334631023,0.0774288433255,0.0791590968077,0.0800242235487,0.0782939700666,0.0782939700666,0.0800242235487,0.0774288433255,0.0795916601782,0.0804567869193,0.0795916601782,0.0756985898434,0.0731032096202,0.0718055195086,0.0718055195086,0.0726706462497,0.0726706462497,0.0722380828791,0.0692101392854,0.0661821956917,0.0614239986158,0.0635868154685,0.0653170689506,0.064019378839,0.0644519422095,0.0627216887274,0.0622891253569,0.0627216887274,0.064019378839,0.0661821956917,0.0687775759149,0.0683450125443,0.0700752660265,0.0674798858033,0.0683450125443,0.0709403927675,0.0709403927675,0.0731032096202,0.070507829397,0.070507829397,0.0713729561381,0.0718055195086,0.0687775759149,0.0726706462497,0.0718055195086,0.0726706462497,0.0778614066961,0.076996279955,0.0800242235487,0.0813219136604,0.0795916601782,0.0821870404014,0.0808893502898,0.0800242235487,0.082619603772,0.0787265334371,0.0752660264729,0.0761311532139,0.0739683363613,0.0744008997318,0.0765637165845,0.0735357729907,0.0756985898434,0.0765637165845,0.0761311532139,0.0756985898434,0.0744008997318,0.0744008997318,0.0765637165845,0.0752660264729,0.0739683363613,0.0731032096202,0.0739683363613,0.0748334631023,0.0731032096202,0.0787265334371,0.0782939700666,0.0765637165845,0.0744008997318,0.0735357729907,0.0731032096202,0.0756985898434,0.0761311532139,0.0748334631023,0.0744008997318,0.0722380828791,0.0726706462497,0.0782939700666,0.0782939700666,0.0761311532139,0.0778614066961,0.0787265334371,0.0795916601782,0.0787265334371,0.0787265334371,0.0778614066961,0.0795916601782,0.0748334631023,0.0756985898434,0.0808893502898,0.0804567869193,0.0800242235487,0.076996279955,0.0791590968077,0.0800242235487,0.0787265334371,0.0752660264729,0.0765637165845,0.0748334631023,0.0722380828791,0.0709403927675,0.0696427026559,0.0722380828791,0.070507829397,0.0731032096202,0.0752660264729,0.0813219136604,0.0795916601782,0.082619603772,0.0830521671425,0.0886754909594,0.0917034345532,0.0912708711826,0.0934336880353,0.0947313781469,0.0942988147764,0.0869452374773,0.0860801107362,0.0847824206246,0.0852149839952,0.0795916601782,0.0718055195086,0.0687775759149,0.0679124491738,0.0661821956917,0.0635868154685,0.0653170689506,0.0674798858033,0.0666147590622,0.0648845055801,0.0657496323211,0.0700752660265,0.0731032096202,0.0722380828791,0.0679124491738,0.0692101392854,0.0713729561381,0.0687775759149,0.0687775759149,0.0683450125443,0.0653170689506,0.0648845055801,0.0635868154685,0.0653170689506,0.0674798858033,0.0679124491738,0.0674798858033,0.0679124491738,0.0653170689506,0.0679124491738,0.0700752660265,0.0674798858033,0.0666147590622,0.0622891253569,0.0614239986158,0.0627216887274,0.0674798858033,0.0696427026559,0.0722380828791,0.0718055195086,0.0731032096202,0.0718055195086,0.0726706462497,0.0761311532139,0.0756985898434,0.0761311532139,0.0731032096202,0.076996279955,0.0765637165845,0.0756985898434,0.0761311532139,0.0787265334371,0.0774288433255,0.0752660264729,0.0787265334371,0.0756985898434,0.0752660264729,0.0709403927675,0.0709403927675,0.0713729561381,0.070507829397,0.0700752660265,0.0713729561381,0.0718055195086,0.070507829397,0.0713729561381,0.0700752660265,0.0687775759149,0.0692101392854,0.0661821956917,0.0666147590622,0.0666147590622,0.0657496323211,0.0670473224327,0.0661821956917,0.0692101392854,0.0674798858033,0.0700752660265,0.0731032096202,0.0756985898434,0.0752660264729,0.0778614066961,0.0791590968077,0.0795916601782,0.0778614066961,0.0761311532139,0.0800242235487,0.0813219136604,0.0800242235487,0.0830521671425,0.0821870404014,0.0830521671425,0.08910805433,0.0908383078121,0.0921359979237,0.0925685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m <- 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ycorr <- 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altd  <- c(38, 66, 124, 146, 255, 410, 474, 514, 558)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('01-FLM-GSE48082/gFLM-GFP-replicate-3-DP28-GSM1167552/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) : 38,66,124,146,255,410,474,514,558',bty='n')
dev.off()