# R script for Peak Model
#  -- generated by MACS
p <- c(0.0251833789699,0.0299802130594,0.0359762556713,0.0403733535866,0.044770451502,0.0459696600244,0.0467691323726,0.0439709791538,0.0483680770691,0.0495672855915,0.0483680770691,0.0487678132433,0.0471688685468,0.0451701876761,0.044770451502,0.0475686047209,0.0463693961985,0.0491675494174,0.0467691323726,0.0491675494174,0.051166230288,0.0539643835069,0.0555633282034,0.0595606899446,0.0619591069894,0.0623588431635,0.0635580516859,0.0651569963824,0.0643575240341,0.0635580516859,0.0623588431635,0.0611596346411,0.0627585793376,0.0615593708153,0.0627585793376,0.0603601622929,0.06395778786,0.0643575240341,0.0647572602083,0.0659564687306,0.0659564687306,0.06395778786,0.0659564687306,0.0647572602083,0.0619591069894,0.0623588431635,0.0599604261188,0.057562009074,0.0603601622929,0.0567625367258,0.0591609537705,0.0599604261188,0.057562009074,0.0571622728999,0.0583614814223,0.0587612175964,0.0583614814223,0.0571622728999,0.0555633282034,0.0567625367258,0.0571622728999,0.0567625367258,0.057562009074,0.0623588431635,0.0623588431635,0.0619591069894,0.060759898467,0.0611596346411,0.0587612175964,0.0583614814223,0.0579617452481,0.0587612175964,0.0587612175964,0.0559630643775,0.0555633282034,0.0567625367258,0.0567625367258,0.0571622728999,0.0603601622929,0.0595606899446,0.0595606899446,0.0599604261188,0.0599604261188,0.0615593708153,0.0643575240341,0.060759898467,0.0631583155118,0.0659564687306,0.0663562049048,0.0679551496013,0.0679551496013,0.0659564687306,0.0627585793376,0.06395778786,0.0615593708153,0.0635580516859,0.0643575240341,0.0643575240341,0.0635580516859,0.0651569963824,0.0643575240341,0.0655567325565,0.06395778786,0.0643575240341,0.06395778786,0.0655567325565,0.0643575240341,0.0627585793376,0.0595606899446,0.0571622728999,0.0599604261188,0.0595606899446,0.0623588431635,0.0603601622929,0.0623588431635,0.0603601622929,0.0567625367258,0.0555633282034,0.057562009074,0.0567625367258,0.0547638558551,0.0555633282034,0.0559630643775,0.0567625367258,0.0535646473328,0.051166230288,0.054364119681,0.0519657026363,0.051166230288,0.0535646473328,0.0535646473328,0.0527651749845,0.0515659664621,0.0507664941139,0.0527651749845,0.054364119681,0.0547638558551,0.057562009074,0.0611596346411,0.057562009074,0.0547638558551,0.0563628005516,0.0555633282034,0.0539643835069,0.0527651749845,0.0523654388104,0.0519657026363,0.0527651749845,0.0487678132433,0.0519657026363,0.054364119681,0.0527651749845,0.0531649111586,0.0523654388104,0.0523654388104,0.054364119681,0.0527651749845,0.0507664941139,0.0515659664621,0.0503667579398,0.051166230288,0.0507664941139,0.0491675494174,0.0523654388104,0.051166230288,0.0507664941139,0.0523654388104,0.0531649111586,0.0519657026363,0.0519657026363,0.0495672855915,0.0507664941139,0.0539643835069,0.0535646473328,0.0559630643775,0.0571622728999,0.0563628005516,0.0587612175964,0.0619591069894,0.0615593708153,0.06395778786,0.0623588431635,0.06395778786,0.060759898467,0.0611596346411,0.060759898467,0.0623588431635,0.0587612175964,0.0583614814223,0.0583614814223,0.0567625367258,0.0603601622929,0.0567625367258,0.0595606899446,0.0587612175964,0.0563628005516,0.0539643835069,0.0567625367258,0.057562009074,0.0599604261188,0.0631583155118,0.060759898467,0.0595606899446,0.0563628005516,0.0559630643775,0.057562009074,0.0591609537705,0.0591609537705,0.0559630643775,0.0559630643775,0.0559630643775,0.0591609537705,0.0659564687306,0.0679551496013,0.0699538304719,0.070353566646,0.0695540942978,0.0687546219495,0.0695540942978,0.0695540942978,0.0679551496013,0.0619591069894,0.0567625367258,0.0567625367258,0.0567625367258,0.0579617452481,0.0571622728999,0.054364119681,0.0523654388104,0.0495672855915,0.0451701876761,0.0459696600244,0.0467691323726,0.0487678132433,0.0471688685468,0.0459696600244,0.0463693961985,0.0491675494174,0.0519657026363,0.0523654388104,0.0551635920293,0.0587612175964,0.0603601622929,0.0579617452481,0.0567625367258,0.0555633282034,0.0547638558551,0.0527651749845,0.0523654388104,0.0519657026363,0.0523654388104,0.0495672855915,0.0483680770691,0.0471688685468,0.0455699238503,0.0459696600244,0.0443707153279,0.0475686047209,0.0487678132433,0.0495672855915,0.0507664941139,0.054364119681,0.0551635920293,0.0559630643775,0.0599604261188,0.060759898467,0.06395778786,0.0643575240341,0.0631583155118,0.0647572602083,0.06395778786,0.0603601622929,0.0595606899446,0.0619591069894,0.0603601622929,0.0599604261188,0.060759898467,0.0599604261188,0.060759898467,0.0611596346411,0.0611596346411,0.0623588431635,0.0611596346411,0.0587612175964,0.0587612175964,0.0591609537705,0.0579617452481,0.0559630643775,0.0547638558551,0.0555633282034,0.0535646473328,0.054364119681,0.0539643835069,0.0539643835069,0.0547638558551,0.0567625367258,0.0599604261188,0.06395778786,0.0659564687306,0.06395778786,0.0651569963824,0.0655567325565,0.0683548857754,0.070353566646,0.0719525113425,0.0727519836908,0.0691543581236,0.067155677253,0.0699538304719,0.0699538304719,0.0723522475166,0.0719525113425,0.0695540942978,0.0691543581236,0.067155677253,0.064757260208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m <- 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ycorr <- 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altd  <- c(39, 97, 487, 518, 594)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('ASCL2-FLAG_ChIP_dox+_ctrl_SA-tTA-Ascl2_ESCs-GSM2576035/SRR5445214.36mers.unique.MACS-2.1.0_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) : 39,97,487,518,594',bty='n')
dev.off()