# R script for Peak Model
#  -- generated by MACS
p <- c(0.0286167999381,0.0340117704182,0.0384684851627,0.0438634556428,0.0473819146516,0.046209094982,0.0424560720393,0.0408141245018,0.0422215081054,0.0426906359732,0.0419869441714,0.0415178163036,0.0412832523697,0.0405795605679,0.0419869441714,0.0429251999071,0.0438634556428,0.0436288917089,0.0419869441714,0.0424560720393,0.0459745310481,0.0452708392463,0.0445671474445,0.0438634556428,0.0424560720393,0.040344996634,0.0424560720393,0.0426906359732,0.0440980195767,0.0433943277749,0.0394067408983,0.0384684851627,0.0379993572948,0.0382339212287,0.0387030490966,0.0401104327001,0.0394067408983,0.0408141245018,0.0389376130305,0.0368265376252,0.0377647933609,0.0382339212287,0.0394067408983,0.0389376130305,0.040344996634,0.0408141245018,0.0412832523697,0.0415178163036,0.0433943277749,0.0448017113785,0.0436288917089,0.0452708392463,0.0445671474445,0.043159763841,0.0396413048323,0.0377647933609,0.0370611015591,0.0377647933609,0.0361228458235,0.0356537179556,0.0368265376252,0.0351845900878,0.0361228458235,0.0384684851627,0.0396413048323,0.0410486884358,0.0412832523697,0.0389376130305,0.0396413048323,0.0410486884358,0.040344996634,0.0387030490966,0.0379993572948,0.0377647933609,0.0384684851627,0.0384684851627,0.0396413048323,0.0398758687662,0.0408141245018,0.040344996634,0.0426906359732,0.0443325835106,0.0429251999071,0.0410486884358,0.0401104327001,0.0394067408983,0.0384684851627,0.0387030490966,0.0382339212287,0.0363574097574,0.0349500261539,0.0365919736913,0.0384684851627,0.0405795605679,0.0408141245018,0.0426906359732,0.0438634556428,0.0426906359732,0.0426906359732,0.0443325835106,0.0450362753124,0.0438634556428,0.0452708392463,0.0440980195767,0.0429251999071,0.0424560720393,0.0417523802375,0.0410486884358,0.0412832523697,0.0396413048323,0.0387030490966,0.0382339212287,0.0372956654931,0.0387030490966,0.0417523802375,0.0408141245018,0.0398758687662,0.0417523802375,0.0408141245018,0.0410486884358,0.0401104327001,0.0398758687662,0.0405795605679,0.0394067408983,0.0377647933609,0.0384684851627,0.0394067408983,0.0377647933609,0.0387030490966,0.0401104327001,0.0424560720393,0.0415178163036,0.0408141245018,0.0415178163036,0.0417523802375,0.0412832523697,0.0398758687662,0.043159763841,0.0429251999071,0.0429251999071,0.0422215081054,0.0443325835106,0.0445671474445,0.0436288917089,0.0452708392463,0.0455054031802,0.0455054031802,0.0438634556428,0.0438634556428,0.0419869441714,0.043159763841,0.0426906359732,0.0440980195767,0.0455054031802,0.0457399671141,0.0457399671141,0.0455054031802,0.0445671474445,0.0433943277749,0.0471473507176,0.0480856064533,0.0480856064533,0.0457399671141,0.0469127867837,0.0473819146516,0.0499621179247,0.0509003736603,0.0516040654621,0.0523077572639,0.0513695015282,0.0504312457925,0.0504312457925,0.051838629396,0.0499621179247,0.0466782228498,0.0450362753124,0.0452708392463,0.0469127867837,0.0473819146516,0.0469127867837,0.0459745310481,0.0455054031802,0.0438634556428,0.0452708392463,0.0473819146516,0.0476164785855,0.0452708392463,0.0438634556428,0.0436288917089,0.0419869441714,0.0410486884358,0.0415178163036,0.0422215081054,0.040344996634,0.040344996634,0.0394067408983,0.0412832523697,0.0417523802375,0.0422215081054,0.0436288917089,0.0436288917089,0.0443325835106,0.0424560720393,0.0422215081054,0.043159763841,0.0433943277749,0.0433943277749,0.0440980195767,0.0433943277749,0.0452708392463,0.0471473507176,0.0473819146516,0.0497275539908,0.0516040654621,0.0516040654621,0.0527768851317,0.0527768851317,0.0530114490656,0.0539497048013,0.0541842687352,0.054653396603,0.0537151408674,0.0527768851317,0.0530114490656,0.0527768851317,0.0520731933299,0.0532460129995,0.0520731933299,0.0527768851317,0.0537151408674,0.0520731933299,0.0537151408674,0.0560607802066,0.0555916523387,0.0539497048013,0.0544188326691,0.051838629396,0.0525423211978,0.0523077572639,0.0494929900568,0.0513695015282,0.0499621179247,0.0499621179247,0.0511349375943,0.0525423211978,0.0525423211978,0.0558262162726,0.0574681638101,0.0579372916779,0.0600483670832,0.0591101113475,0.0612211867528,0.0612211867528,0.0621594424884,0.0614557506867,0.063332262158,0.0619248785545,0.0614557506867,0.0598138031493,0.0600483670832,0.0584064195457,0.0591101113475,0.060517494951,0.0598138031493,0.0623940064224,0.0612211867528,0.0647396457615,0.0642705178937,0.0668507211668,0.0675544129686,0.0699000523078,0.0677889769025,0.0673198490347,0.0677889769025,0.0675544129686,0.0675544129686,0.0652087736294,0.066381593299,0.0642705178937,0.063566826092,0.0649742096955,0.0677889769025,0.0670852851007,0.0661470293651,0.0666161572329,0.0677889769025,0.0684926687042,0.0694309244399,0.0696654883738,0.0706037441095,0.0703691801756,0.0689617965721,0.0710728719774,0.072011127713,0.0727148195148,0.0743567670522,0.075060458854,0.075060458854,0.0783443539288,0.0774060981932,0.0785789178627,0.0816282490037,0.0849121440786,0.0879614752195,0.0891342948891,0.0886651670212,0.0910108063604,0.0931218817657,0.0954675211049,0.0964057768406,0.0947638293031,0.0931218817657,0.0905416784926,0.091949062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m <- 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ycorr <- 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altd  <- c(227)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('DAPseq_of_N_crassa_NCU03725_VIB-1.1x36mers.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) : 227',bty='n')
dev.off()