# R script for Peak Model
#  -- generated by MACS
p <- c(0.0232298671659,0.0267906497241,0.0305209933566,0.0345904591375,0.0388294859926,0.0393381692152,0.0395077302894,0.0401859745862,0.0405250967346,0.0413729021056,0.0398468524378,0.0389990470668,0.0401859745862,0.0396772913636,0.0393381692152,0.0383208027699,0.0374729973989,0.0364556309537,0.0366251920279,0.0345904591375,0.0356078255827,0.0373034363247,0.0359469477311,0.0357773866569,0.0352687034343,0.0359469477311,0.0362860698795,0.0364556309537,0.0352687034343,0.0356078255827,0.0347600202117,0.0364556309537,0.0364556309537,0.0374729973989,0.0389990470668,0.0386599249184,0.0388294859926,0.0388294859926,0.0378121195473,0.0381512416957,0.0393381692152,0.0374729973989,0.0384903638442,0.0378121195473,0.0379816806215,0.0379816806215,0.0388294859926,0.0401859745862,0.041712024254,0.0418815853282,0.0423902685508,0.041712024254,0.0410337799572,0.0403555356604,0.0396772913636,0.039168608141,0.0381512416957,0.0376425584731,0.0378121195473,0.0367947531021,0.0374729973989,0.0378121195473,0.0386599249184,0.0395077302894,0.0389990470668,0.0396772913636,0.040864218883,0.0403555356604,0.0396772913636,0.0412033410314,0.040016413512,0.040016413512,0.0395077302894,0.0383208027699,0.0389990470668,0.0384903638442,0.0383208027699,0.0389990470668,0.039168608141,0.0389990470668,0.0386599249184,0.0386599249184,0.0388294859926,0.0393381692152,0.0379816806215,0.0378121195473,0.0371338752505,0.0359469477311,0.0371338752505,0.0361165088053,0.0354382645085,0.0342513369891,0.0342513369891,0.0344208980633,0.0342513369891,0.0342513369891,0.0357773866569,0.0361165088053,0.0354382645085,0.0371338752505,0.0379816806215,0.0403555356604,0.0389990470668,0.040016413512,0.0406946578088,0.0442554403671,0.0430685128476,0.0440858792929,0.0439163182187,0.0430685128476,0.0427293906992,0.0418815853282,0.042559829625,0.0415424631798,0.041712024254,0.0396772913636,0.0410337799572,0.041712024254,0.0412033410314,0.0415424631798,0.0437467571445,0.0444250014413,0.0444250014413,0.0457814900349,0.0456119289607,0.0451032457381,0.0456119289607,0.0449336846639,0.0449336846639,0.0442554403671,0.043407634996,0.0422207074766,0.0422207074766,0.0420511464024,0.0432380739218,0.0444250014413,0.0415424631798,0.041712024254,0.0428989517734,0.0452728068123,0.0435771960703,0.0435771960703,0.0447641235897,0.0439163182187,0.0420511464024,0.0418815853282,0.0439163182187,0.0415424631798,0.0401859745862,0.0381512416957,0.0395077302894,0.0422207074766,0.0412033410314,0.0428989517734,0.0442554403671,0.0439163182187,0.0447641235897,0.0490031504448,0.0501900779642,0.05002051689,0.0493422725932,0.0464597343317,0.0471379786285,0.0469684175543,0.0481553450737,0.0478162229253,0.0471379786285,0.0459510511091,0.0467988564801,0.0469684175543,0.0479857839995,0.049172711519,0.05002051689,0.049172711519,0.049172711519,0.0506987611868,0.0498509558158,0.0490031504448,0.0474771007769,0.0488335893706,0.0495118336674,0.0493422725932,0.0493422725932,0.0498509558158,0.0496813947416,0.0476466618511,0.0488335893706,0.0506987611868,0.0530726162256,0.0540899826709,0.0532421772998,0.0547682269677,0.0552769101903,0.0557855934129,0.0552769101903,0.0579898873775,0.0579898873775,0.0571420820065,0.0559551544871,0.0557855934129,0.0573116430807,0.0581594484517,0.0578203263033,0.0573116430807,0.0566333987839,0.0568029598581,0.0568029598581,0.0566333987839,0.0569725209323,0.0568029598581,0.0561247155613,0.0545986658935,0.0554464712645,0.0571420820065,0.0584985706001,0.0571420820065,0.0578203263033,0.0584985706001,0.0579898873775,0.0573116430807,0.0590072538228,0.0598550591938,0.062568036381,0.0622289142326,0.0629071585294,0.0646027692715,0.063415841752,0.0646027692715,0.0678244296813,0.0695200404234,0.0683331129039,0.0695200404234,0.0676548686071,0.0664679410877,0.0669766243103,0.0659592578651,0.0669766243103,0.0661288189393,0.0642636471231,0.0644332081973,0.0652810135683,0.0642636471231,0.0646027692715,0.0678244296813,0.0671461853845,0.0696896014976,0.0710460900912,0.0710460900912,0.0727417008332,0.0727417008332,0.0735895062042,0.0754546780205,0.0781676552077,0.0776589719851,0.0798632659498,0.0803719491724,0.0815588766918,0.084271853879,0.0830849263596,0.0832544874338,0.084271853879,0.0818979988402,0.0774894109109,0.0783372162819,0.0763024833915,0.0751155558721,0.0749459947979,0.072572139759,0.0747764337237,0.0757938001689,0.0747764337237,0.0769807276883,0.0796937048756,0.0783372162819,0.0796937048756,0.0803719491724,0.0815588766918,0.0827458042112,0.0830849263596,0.0835936095822,0.0835936095822,0.0852892203243,0.0839327317306,0.0874935142889,0.0885108807341,0.0878326364373,0.0896978082536,0.0929194686634,0.0927499075892,0.0951237626281,0.0966498122959,0.0966498122959,0.0997019116316,0.0991932284089,0.100380155928,0.103093133116,0.103093133116,0.101397522374,0.101397522374,0.100719278077,0.101567083448,0.103093133116,0.102414888819,0.103771377412,0.104449621709,0.103093133116,0.102414888819,0.104788743858,0.104958304932,0.105127866006,0.105636549229,0.104788743858,0.10851908749,0.110553820381,0.112588553271,0.114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m <- 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ycorr <- 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altd  <- c(256)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('DAPseq_of_N_crassa_NCU08042_CLR-2.1x36mers.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) : 256',bty='n')
dev.off()