# R script for Peak Model
#  -- generated by MACS
p <- c(0.0448932289372,0.0531236542423,0.0603564522378,0.0675892502332,0.0744063701829,0.0737412853098,0.0736581497006,0.0731593360458,0.0731593360458,0.0725773867818,0.0724942511726,0.0722448443452,0.0720785731269,0.0718291662995,0.0718291662995,0.0721617087361,0.0718291662995,0.0716628950812,0.0710809458172,0.0709978102081,0.0707484033806,0.0700833185075,0.0700001828983,0.0698339116801,0.0699170472892,0.0695845048526,0.0706652677715,0.0705821321623,0.0701664541166,0.0695845048526,0.0697507760709,0.0691688268069,0.0689194199795,0.0690856911978,0.0697507760709,0.0703327253349,0.0700833185075,0.0706652677715,0.0717460306903,0.0729099292183,0.0728267936092,0.0733256072641,0.0742400989646,0.0745726414012,0.0748220482286,0.0749883194469,0.0754039974926,0.0758196755383,0.0751545906652,0.0750714550561,0.0759859467566,0.0763184891932,0.0757365399292,0.0757365399292,0.0749051838378,0.0740738277463,0.0739075565281,0.0743232345738,0.0749883194469,0.0750714550561,0.0742400989646,0.0740738277463,0.0746557770103,0.0746557770103,0.0751545906652,0.0751545906652,0.0742400989646,0.0734087428732,0.0740738277463,0.0734087428732,0.0731593360458,0.0730762004366,0.0727436580001,0.0728267936092,0.0730762004366,0.0735750140915,0.0746557770103,0.0752377262743,0.0741569633555,0.0752377262743,0.0757365399292,0.0759028111475,0.0756534043201,0.0751545906652,0.0749051838378,0.0741569633555,0.0738244209189,0.0734087428732,0.0741569633555,0.0745726414012,0.0744895057921,0.0741569633555,0.0735750140915,0.0739906921372,0.0743232345738,0.0746557770103,0.0744895057921,0.0741569633555,0.0745726414012,0.0729930648275,0.0728267936092,0.0728267936092,0.0729930648275,0.0722448443452,0.0717460306903,0.0714966238629,0.0709978102081,0.0719954375178,0.0708315389898,0.0714134882538,0.0712472170355,0.0715797594721,0.0727436580001,0.0739075565281,0.0734087428732,0.0733256072641,0.0737412853098,0.0724942511726,0.0727436580001,0.0724942511726,0.0721617087361,0.0723279799543,0.0720785731269,0.0713303526446,0.0721617087361,0.0724942511726,0.0733256072641,0.0732424716549,0.0734918784823,0.0734918784823,0.0743232345738,0.0739906921372,0.0738244209189,0.0739075565281,0.0740738277463,0.0739906921372,0.0732424716549,0.0735750140915,0.0733256072641,0.0732424716549,0.0723279799543,0.0731593360458,0.0734918784823,0.0741569633555,0.0738244209189,0.0733256072641,0.0735750140915,0.0739075565281,0.0744895057921,0.0754871331018,0.0763184891932,0.0756534043201,0.0757365399292,0.0751545906652,0.0748220482286,0.0754039974926,0.0746557770103,0.0750714550561,0.0737412853098,0.0724942511726,0.0730762004366,0.0727436580001,0.0726605223909,0.0723279799543,0.0730762004366,0.0738244209189,0.0740738277463,0.0728267936092,0.0739906921372,0.0753208618835,0.0756534043201,0.0759859467566,0.0759028111475,0.0769004384572,0.0771498452846,0.0769004384572,0.0778149301578,0.0792282355132,0.0786462862492,0.0778980657669,0.0768173028481,0.0770667096755,0.0763184891932,0.0759859467566,0.0760690823658,0.0765678960206,0.0769835740663,0.0770667096755,0.0772329808938,0.0774823877212,0.0780643369852,0.0782306082035,0.0785631506401,0.0779812013761,0.0776486589395,0.0771498452846,0.0769835740663,0.0771498452846,0.0773161165029,0.0771498452846,0.0772329808938,0.0773161165029,0.0773992521121,0.0784800150309,0.0777317945486,0.0774823877212,0.0770667096755,0.0763184891932,0.0762353535841,0.0762353535841,0.0755702687109,0.0751545906652,0.0747389126195,0.0743232345738,0.0752377262743,0.0749051838378,0.0745726414012,0.0744895057921,0.0744895057921,0.0743232345738,0.0748220482286,0.0759859467566,0.0772329808938,0.0774823877212,0.0771498452846,0.0772329808938,0.0775655233303,0.0782306082035,0.0783137438126,0.0790619642949,0.0793113711223,0.0781474725943,0.0783968794218,0.0785631506401,0.0787294218583,0.0785631506401,0.0781474725943,0.0787294218583,0.0789788286858,0.0788125574675,0.0790619642949,0.0799764559955,0.0798101847772,0.0803089984321,0.0808909476961,0.0818885750058,0.0823873886606,0.0820548462241,0.0818054393966,0.0819717106149,0.0808909476961,0.0806415408686,0.0808078120869,0.0808078120869,0.0810572189143,0.0808078120869,0.0811403545235,0.0806415408686,0.0812234901326,0.0810572189143,0.0815560325692,0.0818054393966,0.0819717106149,0.0813897613509,0.0814728969601,0.0825536598789,0.0832187447521,0.0841332364526,0.0843826432801,0.0847983213258,0.0849645925441,0.0847151857166,0.0842163720618,0.0844657788892,0.0830524735338,0.0829693379246,0.0826367954881,0.0827199310972,0.0833018803612,0.0832187447521,0.0838838296252,0.0837175584069,0.0845489144984,0.0857128130264,0.0877912032549,0.0873755252092,0.0874586608184,0.0871261183818,0.0870429827726,0.0879574744732,0.0883731525189,0.0887056949555,0.0890382373921,0.0889551017829,0.0887888305646,0.0887888305646,0.0888719661738,0.0892045086104,0.0892045086104,0.0889551017829,0.0889551017829,0.0893707798286,0.0892045086104,0.0892045086104,0.0891213730012,0.0892045086104,0.0897033222652,0.0901190003109,0.0906178139658,0.0911166276206,0.0912828988389,0.0920311193212,0.0914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m <- 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ycorr <- 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altd  <- c(4, 274)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('DAPseq_of_N_crassa_NCU04731_SAH-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) : 4,274',bty='n')
dev.off()