# R script for Peak Model
#  -- generated by MACS
p <- c(0.0216424417693,0.025720003262,0.0302680526194,0.0335614676712,0.0370117120112,0.0356002484176,0.035129760553,0.0352865898412,0.0362275655703,0.0365412241467,0.0368548827231,0.035913906994,0.0360707362821,0.0374821998758,0.0371685412994,0.0379526877403,0.037639029164,0.0370117120112,0.035913906994,0.0362275655703,0.035913906994,0.0352865898412,0.0343456141121,0.0326204919421,0.033404638383,0.033404638383,0.033404638383,0.0335614676712,0.0337182969594,0.0326204919421,0.0323068333657,0.0337182969594,0.0335614676712,0.0335614676712,0.0340319555358,0.0341887848239,0.0341887848239,0.0345024434003,0.0348161019767,0.0356002484176,0.0366980534349,0.0366980534349,0.0382663463167,0.0392073220458,0.0395209806222,0.0381095170285,0.0385800048931,0.0381095170285,0.0373253705876,0.0366980534349,0.0368548827231,0.0362275655703,0.0356002484176,0.035913906994,0.0341887848239,0.0346592726885,0.0343456141121,0.0343456141121,0.0346592726885,0.0348161019767,0.0340319555358,0.035129760553,0.0332478090948,0.0327773212303,0.0321500040776,0.0332478090948,0.0337182969594,0.0343456141121,0.0348161019767,0.0343456141121,0.0337182969594,0.0327773212303,0.0335614676712,0.0326204919421,0.033404638383,0.0335614676712,0.0323068333657,0.0327773212303,0.0326204919421,0.0326204919421,0.0341887848239,0.0338751262476,0.0337182969594,0.033404638383,0.0338751262476,0.0340319555358,0.0346592726885,0.0330909798067,0.033404638383,0.0332478090948,0.0337182969594,0.0346592726885,0.0346592726885,0.0341887848239,0.0340319555358,0.0340319555358,0.0349729312649,0.0349729312649,0.0352865898412,0.0354434191294,0.035129760553,0.035129760553,0.0354434191294,0.0373253705876,0.0379526877403,0.0373253705876,0.0377958584522,0.0382663463167,0.0379526877403,0.0384231756049,0.0379526877403,0.0381095170285,0.0381095170285,0.0381095170285,0.0366980534349,0.0374821998758,0.0365412241467,0.0379526877403,0.0371685412994,0.0379526877403,0.0381095170285,0.0371685412994,0.0384231756049,0.0379526877403,0.0379526877403,0.0377958584522,0.0381095170285,0.0366980534349,0.0370117120112,0.0363843948585,0.0357570777058,0.0363843948585,0.0345024434003,0.0366980534349,0.0368548827231,0.0370117120112,0.0365412241467,0.0371685412994,0.0385800048931,0.0377958584522,0.0388936634694,0.0381095170285,0.0385800048931,0.037639029164,0.0373253705876,0.0370117120112,0.0388936634694,0.0384231756049,0.0366980534349,0.0374821998758,0.0384231756049,0.0398346391985,0.0406187856395,0.0406187856395,0.0415597613686,0.0407756149276,0.0396778099104,0.0403051270631,0.0406187856395,0.0425007370977,0.0404619563513,0.0404619563513,0.0404619563513,0.0396778099104,0.0384231756049,0.0385800048931,0.0374821998758,0.039364151334,0.0414029320804,0.0409324442158,0.0415597613686,0.0415597613686,0.0418734199449,0.0425007370977,0.0442258592677,0.0457941521495,0.0473624450313,0.0448531764204,0.0435985421149,0.0432848835386,0.0439122006913,0.0439122006913,0.0448531764204,0.0454804935731,0.0446963471322,0.0443826885559,0.042814395674,0.0431280542504,0.0426575663858,0.0448531764204,0.0446963471322,0.0448531764204,0.0434417128268,0.0440690299795,0.044539517844,0.0440690299795,0.0467351278786,0.0489307379132,0.0483034207604,0.0472056157432,0.0473624450313,0.0467351278786,0.0467351278786,0.0451668349968,0.0475192743195,0.0489307379132,0.0478329328959,0.047048786455,0.0492443964895,0.0481465914723,0.0492443964895,0.0492443964895,0.0506558600832,0.0508126893714,0.0498717136423,0.0481465914723,0.0479897621841,0.0464214693022,0.0465782985904,0.0468919571668,0.0462646400141,0.0484602500486,0.047048786455,0.047048786455,0.0454804935731,0.0475192743195,0.0479897621841,0.0512831772359,0.0526946408296,0.0537924458468,0.0531651286941,0.0520673236768,0.0531651286941,0.0533219579823,0.0561448851696,0.0572426901869,0.0580268366278,0.0567722023223,0.0550470801523,0.0544197629996,0.0567722023223,0.0577131780514,0.0578700073396,0.0594383002214,0.0575563487632,0.0573995194751,0.0566153730341,0.0569290316105,0.0575563487632,0.0603792759505,0.0584973244923,0.0589678123569,0.0588109830687,0.0595951295096,0.061633910256,0.0619475688324,0.0638295202906,0.0639863495788,0.0632022031378,0.0611634223915,0.0630453738497,0.0611634223915,0.0624180566969,0.0614770809678,0.0605361052387,0.0595951295096,0.0589678123569,0.0595951295096,0.0613202516796,0.063359032426,0.0632022031378,0.0644568374433,0.0657114717488,0.0663387889015,0.0666524474779,0.0680639110715,0.0704163503943,0.0701026918179,0.0704163503943,0.0691617160888,0.0705731796825,0.0730824482934,0.0738665947343,0.0737097654461,0.0741802533107,0.074493911887,0.072768789717,0.0732392775816,0.0755917169043,0.0768463512098,0.0759053754807,0.074493911887,0.0733961068698,0.0760622047689,0.0776304976507,0.0782578148034,0.0795124491089,0.0818648884316,0.0813944005671,0.0815512298553,0.0820217177198,0.0837468398898,0.086412937789,0.0853151327717,0.0879812306708,0.0895495235526,0.0904904992817,0.0914314750108,0.0947248900627,0.0944112314863,0.0980183051145,0.100213915149,0.100057085861,0.101939037319,0.1014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m <- 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ycorr <- 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altd  <- c(243)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('DAPseq_of_N_crassa_NCU06971_XLR-1A828V_mutant.1x36mers.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) : 243',bty='n')
dev.off()