# R script for Peak Model
#  -- generated by MACS
p <- c(0.0487309871091,0.0567598911637,0.0647887952183,0.0727340648557,0.0808744814666,0.0808187251885,0.0807908470494,0.0804005531023,0.0804841875195,0.0804005531023,0.0802611624069,0.0801217717115,0.0801775279897,0.0802332842678,0.0801496498506,0.0801496498506,0.0800381372943,0.0801217717115,0.079954502877,0.0799266247379,0.0799266247379,0.0799823810161,0.0799266247379,0.0799266247379,0.0798151121816,0.0798429903207,0.0801496498506,0.0802054061287,0.0803726749632,0.0804841875195,0.0807072126321,0.0807072126321,0.081013872162,0.0811253847183,0.0812368972746,0.0814320442482,0.0815435568045,0.0815435568045,0.0818223381953,0.0818502163344,0.0817665819171,0.0819896070298,0.0814878005263,0.08137628797,0.0814599223873,0.0813205316919,0.0809859940229,0.08137628797,0.0812090191356,0.0810975065792,0.0808744814666,0.0809859940229,0.0813484098309,0.0816271912217,0.0816271912217,0.0815156786654,0.0814320442482,0.0810975065792,0.0810417503011,0.0810417503011,0.0810696284402,0.0808744814666,0.0807350907712,0.0804563093804,0.0800102591552,0.0798987465989,0.0795642089299,0.0792854275391,0.0788393773139,0.0786163522013,0.0785048396449,0.0782539363932,0.0782539363932,0.0783375708105,0.0785884740622,0.0785605959231,0.0788393773139,0.0791739149828,0.0793411838173,0.0793411838173,0.0792854275391,0.0792854275391,0.0793411838173,0.079229671261,0.0792575494001,0.0793690619564,0.0797593559035,0.0796199652081,0.0794805745127,0.0789787680093,0.079229671261,0.0795363307908,0.0792854275391,0.0791181587047,0.0789787680093,0.078895133592,0.0787557428967,0.0786442303403,0.0787557428967,0.0794248182345,0.0794248182345,0.0792575494001,0.0796199652081,0.0799823810161,0.0802611624069,0.0803726749632,0.0804284312414,0.0804563093804,0.080651456354,0.0805678219368,0.080289040546,0.080289040546,0.0799823810161,0.0798708684598,0.0799266247379,0.0798151121816,0.0798151121816,0.0799266247379,0.0800102591552,0.0799823810161,0.0801496498506,0.0799266247379,0.079954502877,0.0800381372943,0.0801217717115,0.0802611624069,0.0802332842678,0.0804005531023,0.0804284312414,0.0807350907712,0.0807908470494,0.0811253847183,0.0811532628574,0.0808466033275,0.0805120656586,0.0805120656586,0.0804841875195,0.0804841875195,0.0805120656586,0.0805120656586,0.0805120656586,0.0807350907712,0.0809581158838,0.0812926535528,0.0813205316919,0.0813205316919,0.0811532628574,0.0810975065792,0.080651456354,0.080289040546,0.0800660154333,0.0798708684598,0.0798429903207,0.0796478433472,0.0795642089299,0.0794805745127,0.0797872340426,0.0797035996253,0.0797593559035,0.0797872340426,0.0800660154333,0.0799823810161,0.0797593559035,0.0797314777644,0.0798151121816,0.0797872340426,0.0794805745127,0.0793411838173,0.0797035996253,0.0798151121816,0.0798429903207,0.0799266247379,0.0799823810161,0.0800660154333,0.0802332842678,0.080289040546,0.080289040546,0.0804563093804,0.0799823810161,0.079592087069,0.0793133056782,0.0790066461484,0.0789787680093,0.078867255453,0.0787836210357,0.0786721084794,0.0788114991748,0.0786999866185,0.0790902805656,0.0793690619564,0.0794805745127,0.0795084526518,0.0794248182345,0.0795363307908,0.0794805745127,0.0795084526518,0.0794805745127,0.0795084526518,0.0792854275391,0.0792575494001,0.0794526963736,0.0794526963736,0.0796757214862,0.0797593559035,0.0800938935724,0.0801496498506,0.0803447968241,0.0804841875195,0.0804284312414,0.0808187251885,0.0808744814666,0.0809859940229,0.0809581158838,0.0807072126321,0.0804563093804,0.0807072126321,0.0805678219368,0.0805120656586,0.0806793344931,0.0804284312414,0.0802332842678,0.0802054061287,0.0801217717115,0.0801496498506,0.0801775279897,0.0799823810161,0.0800938935724,0.0802054061287,0.080289040546,0.0803726749632,0.0806235782149,0.0809023596057,0.0811253847183,0.08137628797,0.0813484098309,0.0812926535528,0.0812926535528,0.0812368972746,0.0811811409965,0.0812090191356,0.0813205316919,0.0813205316919,0.0813205316919,0.0813205316919,0.08137628797,0.081738703778,0.0818780944734,0.0819338507516,0.0821011195861,0.0822683884205,0.0822683884205,0.0819338507516,0.0819059726125,0.0819338507516,0.0821568758642,0.0819896070298,0.0819617288907,0.0821011195861,0.0821289977251,0.0821847540033,0.0823241446987,0.0828259512021,0.082798073063,0.0830489763147,0.0828538293412,0.0829653418975,0.0827701949239,0.0826029260895,0.082798073063,0.0827701949239,0.0825471698113,0.0825192916722,0.0828259512021,0.0828259512021,0.0831883670101,0.0834113921228,0.083857442348,0.0840247111825,0.0839131986262,0.0839131986262,0.0837459297917,0.0836622953745,0.0836901735135,0.08349502654,0.0831883670101,0.0829095856193,0.0827701949239,0.0826865605067,0.0827423167849,0.0827701949239,0.0828817074803,0.082798073063,0.082435657255,0.0826865605067,0.0829932200366,0.083160488871,0.0830489763147,0.083132610732,0.083160488871,0.0832162451492,0.083160488871,0.0834671484009,0.0831047325929,0.0828538293412,0.0825471698113,0.0822962665596,0.0821289977251,0.0818780944734,0.081738703778,0.081710825639,0.0818223381953,0.0816550693608,0.0822405102815,0.0822126321424,0.0822683884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m <- 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ycorr <- 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altd  <- c(43, 99, 588)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('91-LFY-GSE96806/LFYGR-GSM2544348/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) : 43,99,588',bty='n')
dev.off()