# R script for Peak Model
#  -- generated by MACS
p <- c(0.0482116572154,0.0564007898493,0.0643814718343,0.0724812684758,0.0802534998119,0.0801343851555,0.0796877051936,0.0792112465676,0.079062353247,0.0790921319111,0.079062353247,0.0788836812623,0.07930058256,0.07930058256,0.0797174838577,0.0798068198501,0.0801939424837,0.0803726144684,0.0805810651173,0.0806108437814,0.080759737102,0.0803130571402,0.0801343851555,0.0798961558425,0.0799854918348,0.0798068198501,0.079777041186,0.0801641638196,0.0802832784761,0.0798068198501,0.0795685905371,0.0803130571402,0.0802534998119,0.0804917291249,0.0803726144684,0.0807299584379,0.0808192944303,0.0806406224455,0.0807001797738,0.0811170810715,0.0812064170639,0.0808788517585,0.0809681877509,0.0808490730944,0.0807001797738,0.0804321717967,0.0806108437814,0.0810277450792,0.0806704011097,0.0804619504608,0.0803428358043,0.0803428358043,0.0801641638196,0.0802534998119,0.0801046064913,0.0800748278272,0.0797472625219,0.0794792545447,0.0798068198501,0.0796281478654,0.0797472625219,0.0797174838577,0.0797472625219,0.0797174838577,0.0799557131707,0.080015270499,0.080015270499,0.0799854918348,0.0795983692012,0.0797472625219,0.0798365985142,0.0799259345066,0.079777041186,0.0794792545447,0.0792708038959,0.0794494758806,0.0796579265295,0.079538811873,0.0794494758806,0.0792410252318,0.0789432385905,0.0790027959188,0.0787050092775,0.0788539025982,0.0792112465676,0.0788539025982,0.0789432385905,0.0789432385905,0.0793601398883,0.0798663771783,0.0801641638196,0.0796281478654,0.0800748278272,0.0799854918348,0.0797472625219,0.0801641638196,0.080015270499,0.0798961558425,0.0796877051936,0.079538811873,0.0792410252318,0.079538811873,0.0793899185524,0.0793601398883,0.0797174838577,0.0793899185524,0.0792410252318,0.0792112465676,0.0794792545447,0.0793899185524,0.079777041186,0.0799557131707,0.0801641638196,0.0804321717967,0.0801939424837,0.0800748278272,0.0802832784761,0.0804619504608,0.0803130571402,0.0802534998119,0.0801343851555,0.0802534998119,0.0798365985142,0.0795685905371,0.0794196972165,0.0798663771783,0.0799557131707,0.0796281478654,0.0796877051936,0.0798068198501,0.0798365985142,0.0795685905371,0.0797174838577,0.0794196972165,0.0791219105753,0.0787050092775,0.0787050092775,0.078824123934,0.0784965586287,0.0784965586287,0.0781987719874,0.0781094359951,0.0780201000027,0.0786454519493,0.0789730172547,0.0790325745829,0.0787645666058,0.0791516892394,0.0796281478654,0.079538811873,0.0795685905371,0.0801343851555,0.0802832784761,0.0803428358043,0.0804917291249,0.0805810651173,0.080997966415,0.0810277450792,0.0808192944303,0.0811170810715,0.081236195728,0.0807895157662,0.0805512864532,0.0803130571402,0.080015270499,0.0800748278272,0.0797174838577,0.0792410252318,0.0793303612241,0.0792112465676,0.0792410252318,0.0790325745829,0.0791516892394,0.0787645666058,0.0788539025982,0.0785858946211,0.0787645666058,0.0789432385905,0.0787645666058,0.0786156732852,0.0781392146592,0.0782583293157,0.0785263372928,0.078824123934,0.0791814679035,0.0795090332089,0.0796281478654,0.0797472625219,0.0796579265295,0.0795090332089,0.0803130571402,0.0803726144684,0.0802237211478,0.0807001797738,0.0805215077891,0.0802832784761,0.0802534998119,0.0799557131707,0.0803130571402,0.0806108437814,0.0805810651173,0.0804917291249,0.0805215077891,0.0801641638196,0.0802534998119,0.0806704011097,0.0804619504608,0.0805810651173,0.0806704011097,0.0805512864532,0.080759737102,0.0809086304227,0.0809681877509,0.0807299584379,0.0804917291249,0.0802832784761,0.0804619504608,0.0806704011097,0.0802237211478,0.0803428358043,0.0799557131707,0.0800450491631,0.079777041186,0.080015270499,0.0802237211478,0.0800748278272,0.0803428358043,0.0804619504608,0.0805810651173,0.0808788517585,0.0807895157662,0.0810277450792,0.0815339823692,0.0816233183616,0.081474425041,0.0820104409952,0.0815339823692,0.0811468597356,0.081474425041,0.0814148677128,0.0818317690105,0.0817722116822,0.0818019903464,0.0822188916441,0.0824571209571,0.0821593343158,0.0825166782853,0.0829633582472,0.0827846862624,0.0826060142777,0.0824571209571,0.0822784489723,0.0822784489723,0.0822188916441,0.0822784489723,0.0823082276364,0.0822486703082,0.0823975636288,0.0825166782853,0.0825166782853,0.0820104409952,0.0822486703082,0.0822486703082,0.0818913263387,0.0817424330181,0.0812659743921,0.0813553103845,0.0809384090868,0.0808788517585,0.080759737102,0.0810575237433,0.0808490730944,0.0808788517585,0.0808490730944,0.0808788517585,0.0811468597356,0.0809681877509,0.0809086304227,0.0809384090868,0.0810575237433,0.0810277450792,0.0811170810715,0.0810873024074,0.0810873024074,0.0813553103845,0.0817424330181,0.0819806623311,0.0820699983235,0.0821593343158,0.0824273422929,0.0825762356136,0.0829038009189,0.0829038009189,0.0833207022166,0.0833504808808,0.0829931369113,0.0829633582472,0.0833802595449,0.0831420302319,0.0831122515678,0.0829038009189,0.0828740222548,0.0832611448884,0.0834993742014,0.0835589315296,0.0839162754991,0.0837673821785,0.0831420302319,0.0834695955373,0.0837673821785,0.0844225127892,0.0846011847739,0.0842736194686,0.0838269395067,0.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m <- 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ycorr <- 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altd  <- c(0, 39, 91, 114, 140, 205, 499, 530, 560)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('36-JAG-GSE51537/JAG-GFP-replicate-3-GSM1247501/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) : 0,39,91,114,140,205,499,530,560',bty='n')
dev.off()