# R script for Peak Model
#  -- generated by MACS
p <- c(0.0320276408246,0.0383361155324,0.0456151248107,0.0538646686595,0.0582320742265,0.0553204705152,0.0562910050856,0.0533794013743,0.0562910050856,0.0587173415117,0.0582320742265,0.0567762723708,0.0553204705152,0.0528941340891,0.0562910050856,0.0606584106526,0.0645405489344,0.0664816180752,0.0679374199309,0.0713342909274,0.0752164292092,0.0771574983501,0.0757016964944,0.0776427656353,0.0771574983501,0.0732753600683,0.0718195582127,0.0713342909274,0.0713342909274,0.0684226872161,0.0669668853605,0.06599635079,0.06599635079,0.06599635079,0.0664816180752,0.0669668853605,0.0664816180752,0.0679374199309,0.0698784890718,0.0713342909274,0.0713342909274,0.0737606273535,0.0766722310649,0.0761869637796,0.0732753600683,0.0723048254979,0.0723048254979,0.070363756357,0.0684226872161,0.0669668853605,0.0679374199309,0.06599635079,0.0655110835048,0.0635700143639,0.0669668853605,0.0684226872161,0.0689079545013,0.0693932217866,0.0698784890718,0.0689079545013,0.0655110835048,0.0640552816491,0.061628945223,0.0621142125082,0.0611436779378,0.0577468069413,0.0562910050856,0.0577468069413,0.0567762723708,0.0567762723708,0.061628945223,0.0669668853605,0.0718195582127,0.0723048254979,0.0727900927831,0.074731161924,0.0727900927831,0.0713342909274,0.0689079545013,0.0679374199309,0.0645405489344,0.0611436779378,0.0596878760821,0.0606584106526,0.0596878760821,0.0601731433674,0.0630847470787,0.061628945223,0.0684226872161,0.0732753600683,0.0737606273535,0.0727900927831,0.0708490236422,0.0713342909274,0.0713342909274,0.0757016964944,0.0766722310649,0.0805543693466,0.0786133002058,0.0732753600683,0.0771574983501,0.0786133002058,0.0800691020614,0.079098567491,0.0805543693466,0.074731161924,0.0766722310649,0.0742458946388,0.0732753600683,0.0737606273535,0.070363756357,0.0693932217866,0.0669668853605,0.0645405489344,0.0621142125082,0.0611436779378,0.057261539656,0.0562910050856,0.0528941340891,0.0553204705152,0.0543499359447,0.0528941340891,0.0528941340891,0.0533794013743,0.0533794013743,0.0558057378004,0.0562910050856,0.0582320742265,0.0606584106526,0.0592026087969,0.0592026087969,0.0601731433674,0.0596878760821,0.0596878760821,0.0640552816491,0.0621142125082,0.0635700143639,0.0621142125082,0.0625994797935,0.0645405489344,0.0669668853605,0.0732753600683,0.0732753600683,0.0742458946388,0.0698784890718,0.0727900927831,0.070363756357,0.0742458946388,0.0742458946388,0.0723048254979,0.0708490236422,0.0679374199309,0.0708490236422,0.0718195582127,0.0732753600683,0.0708490236422,0.0732753600683,0.0674521526457,0.0669668853605,0.0684226872161,0.0689079545013,0.06599635079,0.0645405489344,0.0698784890718,0.070363756357,0.0708490236422,0.0689079545013,0.070363756357,0.0664816180752,0.0664816180752,0.0669668853605,0.0640552816491,0.0635700143639,0.0577468069413,0.057261539656,0.0601731433674,0.061628945223,0.0621142125082,0.0674521526457,0.0650258162196,0.061628945223,0.0621142125082,0.0630847470787,0.0630847470787,0.0621142125082,0.0630847470787,0.0630847470787,0.0625994797935,0.0621142125082,0.0635700143639,0.0635700143639,0.0645405489344,0.0625994797935,0.0635700143639,0.0625994797935,0.0601731433674,0.0592026087969,0.0596878760821,0.0587173415117,0.0621142125082,0.0645405489344,0.0669668853605,0.0693932217866,0.0679374199309,0.0698784890718,0.0708490236422,0.0684226872161,0.0674521526457,0.0664816180752,0.0630847470787,0.0625994797935,0.0640552816491,0.0650258162196,0.0640552816491,0.0630847470787,0.0630847470787,0.0664816180752,0.0708490236422,0.0698784890718,0.0693932217866,0.0693932217866,0.0679374199309,0.0689079545013,0.0737606273535,0.074731161924,0.0761869637796,0.0742458946388,0.0698784890718,0.0693932217866,0.0708490236422,0.070363756357,0.0708490236422,0.0679374199309,0.0625994797935,0.0630847470787,0.0592026087969,0.0587173415117,0.0582320742265,0.0601731433674,0.0587173415117,0.0601731433674,0.0606584106526,0.061628945223,0.0640552816491,0.0630847470787,0.0669668853605,0.0689079545013,0.0718195582127,0.0723048254979,0.074731161924,0.0752164292092,0.0723048254979,0.074731161924,0.0742458946388,0.0727900927831,0.0693932217866,0.0693932217866,0.0689079545013,0.074731161924,0.0718195582127,0.0737606273535,0.0757016964944,0.0742458946388,0.0766722310649,0.0805543693466,0.083465973058,0.0829807057727,0.0849217749136,0.0829807057727,0.0849217749136,0.0805543693466,0.0805543693466,0.0795838347762,0.0786133002058,0.074731161924,0.0737606273535,0.0718195582127,0.0723048254979,0.0669668853605,0.0689079545013,0.0698784890718,0.0718195582127,0.0718195582127,0.0713342909274,0.0727900927831,0.0727900927831,0.0757016964944,0.074731161924,0.0757016964944,0.0752164292092,0.0732753600683,0.0723048254979,0.0727900927831,0.0757016964944,0.0766722310649,0.0771574983501,0.0771574983501,0.0766722310649,0.0766722310649,0.0742458946388,0.0771574983501,0.0771574983501,0.0776427656353,0.0757016964944,0.0795838347762,0.0786133002058,0.0795838347762,0.0824954384875,0.0854070421988,0.0868628440545,0.0883186459102,0.0897744477658,0.0922007841919,0.0922007841919,0.090744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m <- 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ycorr <- 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xcorr <- 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altd  <- c(35, 77, 157, 233, 280, 352, 405, 470, 518, 581)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('C2C12-myoblast-H3K27ac-AM_39113_31814008-RT_Fix_5403-5933_IP_F2-17873.mm10.36mers.unique.MACS-2.1.0.p1e-1_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) : 35,77,157,233,280,352,405,470,518,581',bty='n')
dev.off()