# R script for Peak Model
#  -- generated by MACS
p <- c(0.0477233725835,0.055759691801,0.0639608585921,0.0718735421293,0.0796625899862,0.0796213780927,0.0795801661993,0.0800747089204,0.0804868278546,0.0806516754283,0.0806104635349,0.0808577348954,0.0809813705757,0.0813522776165,0.0818468203376,0.0820528798047,0.0824237868455,0.0823001511652,0.082176515485,0.0820528798047,0.0820940916981,0.0817643965507,0.0816819727639,0.0814759132968,0.0813522776165,0.0814347014033,0.0811874300428,0.0814347014033,0.0813110657231,0.0816819727639,0.0814759132968,0.0817231846573,0.0813110657231,0.0813522776165,0.0811462181494,0.0810637943625,0.0808989467889,0.0809401586823,0.0812286419362,0.0809813705757,0.0811462181494,0.0811462181494,0.0813522776165,0.0813934895099,0.0812286419362,0.0815583370836,0.0817231846573,0.0813934895099,0.0810637943625,0.0808989467889,0.0811874300428,0.0810637943625,0.081105006256,0.0809813705757,0.0813934895099,0.0811462181494,0.081105006256,0.0809813705757,0.0811874300428,0.0810637943625,0.0804868278546,0.0805692516415,0.0804044040678,0.080033497027,0.0797862256664,0.0797862256664,0.0794153186256,0.0796213780927,0.0792504710519,0.0793328948388,0.0796625899862,0.0793328948388,0.0792916829454,0.0794565305191,0.0797038018796,0.0794153186256,0.0794153186256,0.0792504710519,0.0795389543059,0.0793328948388,0.0792092591585,0.0792916829454,0.0792504710519,0.0796213780927,0.0794565305191,0.0796625899862,0.079745013773,0.0796213780927,0.079745013773,0.0798274375599,0.0796213780927,0.0798274375599,0.0800747089204,0.0801159208138,0.0802807683875,0.0803219802809,0.0806928873217,0.0808989467889,0.0808989467889,0.0811874300428,0.0812698538297,0.081105006256,0.0811462181494,0.081105006256,0.0811462181494,0.0813110657231,0.0811874300428,0.0811462181494,0.0811462181494,0.0813110657231,0.0814347014033,0.0819704560178,0.0821353035915,0.0824237868455,0.0825474225258,0.0825474225258,0.0825886344192,0.082671058206,0.082671058206,0.0826298463126,0.0827122700995,0.0822589392718,0.0822177273784,0.0820940916981,0.0820116679113,0.082176515485,0.0823001511652,0.0823825749521,0.0824649987389,0.082671058206,0.0826298463126,0.0827534819929,0.0826298463126,0.0823825749521,0.082176515485,0.0819292441244,0.0816407608705,0.0813522776165,0.0809813705757,0.080528039748,0.0806928873217,0.0807753111086,0.0806928873217,0.0807753111086,0.0806928873217,0.080816523002,0.0807340992152,0.0809813705757,0.0810225824691,0.0811462181494,0.0810225824691,0.0807753111086,0.0806104635349,0.0806104635349,0.080528039748,0.0803631921744,0.080528039748,0.0806104635349,0.0807753111086,0.0809813705757,0.080816523002,0.0809401586823,0.0810637943625,0.0811462181494,0.0813110657231,0.0813522776165,0.0815171251902,0.0814347014033,0.0816407608705,0.0812698538297,0.0812698538297,0.0811462181494,0.0810637943625,0.0808577348954,0.080528039748,0.0801571327072,0.0799098613467,0.079745013773,0.0795801661993,0.0794977424125,0.0794977424125,0.0793741067322,0.0795801661993,0.0796213780927,0.0799510732401,0.0802807683875,0.0803631921744,0.0803631921744,0.0802807683875,0.0804868278546,0.0804044040678,0.0806104635349,0.0806104635349,0.080528039748,0.0804044040678,0.0799922851336,0.0799922851336,0.0797862256664,0.0800747089204,0.0804868278546,0.0807340992152,0.0805692516415,0.0803219802809,0.080528039748,0.080528039748,0.0810225824691,0.0809813705757,0.0811462181494,0.0810637943625,0.0806928873217,0.0805692516415,0.0807753111086,0.0813110657231,0.0810225824691,0.0814759132968,0.0815171251902,0.0816407608705,0.0821353035915,0.0820940916981,0.0824237868455,0.0827534819929,0.08295954146,0.0832480247139,0.0831656009271,0.0830831771403,0.0830831771403,0.0830419652468,0.0827122700995,0.082671058206,0.082671058206,0.0825474225258,0.0823825749521,0.0818056084442,0.0824649987389,0.0820528798047,0.081888032231,0.0820116679113,0.0820940916981,0.0821353035915,0.0818468203376,0.0815583370836,0.0815583370836,0.0818056084442,0.0815171251902,0.081599548977,0.0818468203376,0.0819704560178,0.0819292441244,0.0819292441244,0.0821353035915,0.0823001511652,0.0825474225258,0.0827122700995,0.08295954146,0.0833716603942,0.0832068128205,0.0830419652468,0.0830831771403,0.0832892366074,0.0834128722876,0.0835365079679,0.0835365079679,0.0832480247139,0.0831656009271,0.0830419652468,0.0831656009271,0.0833304485008,0.0835365079679,0.0834540841811,0.0830419652468,0.0831243890337,0.0832068128205,0.0832892366074,0.0830831771403,0.0831656009271,0.0832068128205,0.0834128722876,0.0836601436482,0.0836601436482,0.084031050689,0.0838662031153,0.083742567435,0.0834952960745,0.0836601436482,0.0834952960745,0.0833716603942,0.0831243890337,0.0829183295666,0.0828771176731,0.0828359057797,0.0833304485008,0.0833304485008,0.0837013555416,0.0839898387956,0.0845255934101,0.0847728647706,0.0847316528772,0.0846080171969,0.0849789242377,0.0851849837048,0.085102559918,0.0853086193851,0.0852674074917,0.084814076664,0.0843607458364,0.0845668053035,0.0845255934101,0.0846492290903,0.0843195339429,0.0843195339429,0.0841546863692,0.0841134744758,0.0842783220495,0.0844843815166,0.08469044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m <- 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ycorr <- 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altd  <- c(1, 37, 112, 128, 277, 296, 477, 542, 559, 574, 577)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('98-HDP-GSE89318/HDP2-IP-rep2-GSM2365923/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) : 1,37,112,128,277,296,477,542,559,574,577',bty='n')
dev.off()