# R script for Peak Model
#  -- generated by MACS
p <- c(0.0307607274375,0.0350574639684,0.040916650147,0.0471664487375,0.0524397162982,0.0499007356208,0.0507796135476,0.0508772666506,0.0508772666506,0.0505843073417,0.0501936949298,0.0516584914744,0.0513655321655,0.0492171639,0.049021857694,0.0510725728565,0.0496077763119,0.0501936949298,0.0507796135476,0.0498030825178,0.049119510797,0.0483382859732,0.0483382859732,0.0489242045911,0.0489242045911,0.0486312452821,0.0497054294149,0.0494124701059,0.0485335921792,0.0492171639,0.0500960418268,0.0498030825178,0.0500960418268,0.0499983887238,0.0496077763119,0.0489242045911,0.049119510797,0.0485335921792,0.0489242045911,0.0489242045911,0.0488265514881,0.0504866542387,0.0506819604446,0.0516584914744,0.0516584914744,0.0525373694012,0.0517561445774,0.0530256349161,0.0521467569893,0.0525373694012,0.0530256349161,0.0511702259595,0.0499983887238,0.049119510797,0.0495101232089,0.0488265514881,0.0484359390762,0.0485335921792,0.0489242045911,0.0482406328702,0.0478500204583,0.0486312452821,0.0497054294149,0.0505843073417,0.0505843073417,0.0514631852684,0.0530256349161,0.0520491038863,0.0518537976803,0.0530256349161,0.0529279818131,0.053416247328,0.0539045128428,0.0525373694012,0.0512678790625,0.0496077763119,0.0474594080464,0.0478500204583,0.049119510797,0.0475570611494,0.0479476735613,0.0482406328702,0.0471664487375,0.0471664487375,0.0484359390762,0.049021857694,0.0509749197536,0.0516584914744,0.0508772666506,0.0522444100923,0.0513655321655,0.0512678790625,0.0513655321655,0.0535139004309,0.0535139004309,0.0540021659458,0.0525373694012,0.0514631852684,0.0499007356208,0.049314817003,0.0500960418268,0.0500960418268,0.0502913480327,0.0501936949298,0.0498030825178,0.0485335921792,0.0494124701059,0.0496077763119,0.0515608383714,0.0527326756071,0.053123288019,0.0515608383714,0.0504866542387,0.0499007356208,0.0505843073417,0.0520491038863,0.0526350225042,0.0540021659458,0.0540998190488,0.0545880845637,0.0544904314607,0.0550763500786,0.0558575749024,0.0559552280053,0.0556622686964,0.0551740031815,0.0558575749024,0.0548810438726,0.0543927783577,0.0518537976803,0.0507796135476,0.0517561445774,0.0515608383714,0.0503890011357,0.0504866542387,0.0500960418268,0.0488265514881,0.049021857694,0.0495101232089,0.0507796135476,0.0510725728565,0.0498030825178,0.0485335921792,0.0484359390762,0.0482406328702,0.0481429797673,0.0473617549434,0.0479476735613,0.0470687956345,0.0476547142524,0.0483382859732,0.0489242045911,0.0503890011357,0.0519514507833,0.0514631852684,0.0520491038863,0.0516584914744,0.0515608383714,0.0522444100923,0.0517561445774,0.0517561445774,0.0528303287101,0.0540021659458,0.0540021659458,0.0547833907696,0.0569317590351,0.0568341059321,0.0564434935202,0.057224718344,0.0562481873143,0.0567364528292,0.0551740031815,0.053318594225,0.0517561445774,0.0506819604446,0.049119510797,0.0504866542387,0.0496077763119,0.0482406328702,0.0488265514881,0.0470687956345,0.0466781832226,0.0471664487375,0.0481429797673,0.049314817003,0.0502913480327,0.0516584914744,0.0518537976803,0.0516584914744,0.0525373694012,0.0543927783577,0.0556622686964,0.0565411466232,0.0577129838589,0.0576153307559,0.0563458404173,0.0548810438726,0.0558575749024,0.0565411466232,0.0576153307559,0.0562481873143,0.0558575749024,0.0553693093875,0.0542951252548,0.0542951252548,0.0541974721518,0.0558575749024,0.0567364528292,0.0577129838589,0.0569317590351,0.0583965555798,0.0586895148887,0.0580059431678,0.057322371447,0.0581035962708,0.0600566583303,0.0595683928155,0.0576153307559,0.0547833907696,0.053318594225,0.0512678790625,0.0519514507833,0.0521467569893,0.0530256349161,0.0505843073417,0.0499007356208,0.0495101232089,0.0514631852684,0.0541974721518,0.0540998190488,0.0557599217994,0.0552716562845,0.0570294121381,0.057322371447,0.0595683928155,0.0593730866095,0.0593730866095,0.0583965555798,0.0582012493738,0.0591777804036,0.0598613521244,0.0594707397125,0.0589824741976,0.0580059431678,0.0571270652411,0.057224718344,0.0565411466232,0.0568341059321,0.0561505342113,0.0561505342113,0.0557599217994,0.0552716562845,0.0551740031815,0.0551740031815,0.0558575749024,0.0550763500786,0.057224718344,0.0568341059321,0.0568341059321,0.0576153307559,0.05742002455,0.0584942086827,0.0581035962708,0.0567364528292,0.05742002455,0.0583965555798,0.0582012493738,0.0595683928155,0.061326148669,0.0598613521244,0.0600566583303,0.0607402300512,0.0605449238452,0.0638651293464,0.0634745169345,0.0624979859048,0.0608378831542,0.0587871679917,0.0566387997262,0.0581035962708,0.05742002455,0.0579082900649,0.0584942086827,0.057322371447,0.057224718344,0.0571270652411,0.0571270652411,0.0586895148887,0.061326148669,0.0605449238452,0.0628885983167,0.0623026796988,0.0623026796988,0.0628885983167,0.0624979859048,0.0633768638315,0.0644510479643,0.0645487010673,0.0630839045226,0.065525232097,0.0642557417583,0.0638651293464,0.0644510479643,0.065427578994,0.0679665596714,0.0699196217309,0.0710914589667,0.0705055403488,0.0709938058637,0.0690407438042,0.0704078872458,0.0725562555113,0.0725562555113,0.0708961527607,0.0689430907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m <- 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ycorr <- 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altd  <- c(150)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('48-PIF1-PIF4-GSE43286/PIF1-peaks-2-GSM1059958/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) : 150',bty='n')
dev.off()