# R script for Peak Model
#  -- generated by MACS
p <- c(0.0202900791175,0.024044433893,0.027412310971,0.0306973713995,0.033844404079,0.0340376429277,0.0341204595772,0.0341756706768,0.0339824318281,0.0342860928761,0.0346725705736,0.033844404079,0.0340100373779,0.0348105983227,0.0352522871198,0.03522468157,0.0355007370682,0.0353351037693,0.0357491870166,0.0358043981162,0.0351970760202,0.0362736924631,0.0358043981162,0.0348105983227,0.0348382038725,0.0343965150754,0.0335683485808,0.0338167985292,0.0334855319313,0.0336511652303,0.0337063763299,0.0333198986324,0.033844404079,0.033844404079,0.0340376429277,0.0345897539241,0.0351142593707,0.0349762316216,0.034755387223,0.0347277816732,0.0353074982194,0.0350038371714,0.0348934149721,0.0354731315184,0.0350866538209,0.0348382038725,0.0350038371714,0.0348658094223,0.0352798926696,0.0351970760202,0.0350314427212,0.0350038371714,0.0345621483743,0.0339548262783,0.0338167985292,0.0335959541306,0.0340376429277,0.0339824318281,0.0338996151786,0.0338996151786,0.0337615874295,0.0339272207285,0.0345621483743,0.0346173594739,0.034451726175,0.0343689095256,0.0336235596804,0.0339824318281,0.0340376429277,0.0344793317248,0.0354731315184,0.0350314427212,0.0351142593707,0.0356663703671,0.0359976369649,0.0362736924631,0.0359976369649,0.0360528480646,0.0362736924631,0.0363289035628,0.0357215814667,0.036604959061,0.0365221424115,0.036604959061,0.037212281157,0.0376815755039,0.0391446696444,0.0392550918437,0.0392550918437,0.0394207251426,0.0399452305892,0.0396139639913,0.0396139639913,0.0394759362422,0.0389514307956,0.0390618529949,0.0380128421018,0.037819603253,0.0373503089061,0.0370190423083,0.0364945368617,0.0359976369649,0.0363565091126,0.0364117202122,0.036301298013,0.0359424258653,0.0360804536144,0.0360804536144,0.0358872147657,0.0358596092158,0.0362460869133,0.037212281157,0.0372398867068,0.037515942205,0.0378472088029,0.0380956587512,0.0388134030465,0.0395311473419,0.0406629748845,0.0403317082866,0.040276497187,0.0400280472386,0.0400832583383,0.0398900194895,0.0402212860874,0.0403041027368,0.0403869193863,0.0401660749877,0.0401108638881,0.0404697360357,0.0404973415856,0.0405525526852,0.0409666359325,0.0408286081834,0.0406077637848,0.0404973415856,0.0404421304859,0.0401384694379,0.040276497187,0.0406353693347,0.0405249471354,0.0412702969805,0.0409390303827,0.0414635358292,0.0415739580285,0.0414911413791,0.0408286081834,0.0413255080801,0.0405525526852,0.0404421304859,0.0404973415856,0.0398624139397,0.0400280472386,0.0394483306924,0.039669175091,0.0401384694379,0.0407733970837,0.0402488916372,0.0410770581318,0.0412979025303,0.0411598747812,0.0420432523755,0.0419880412758,0.0424297300729,0.0426781800213,0.0426229689217,0.0420984634751,0.0424573356228,0.0419052246264,0.042264096774,0.0421812801246,0.0418500135267,0.0421812801246,0.0426229689217,0.0423193078737,0.0423193078737,0.0430094466191,0.0436167687152,0.044720990708,0.0449142295567,0.0457423960513,0.0468190124943,0.0466809847452,0.0478128122878,0.0483097121845,0.0484477399336,0.0485581621329,0.0485305565831,0.0472883068412,0.0472054901917,0.0472607012914,0.0462116903982,0.0462945070477,0.0456871849517,0.0457147905015,0.0464601403466,0.0465981680957,0.046404929247,0.0475919678892,0.0471226735423,0.0471502790921,0.0474539401401,0.0481992899853,0.0476747845387,0.0484753454835,0.0481716844354,0.0481992899853,0.0488066120813,0.0488894287308,0.0495243563766,0.0499108340741,0.0497175952253,0.0499384396239,0.0502144951221,0.0497452007752,0.0495795674762,0.0499108340741,0.0496899896755,0.0491654842289,0.0492759064282,0.0494139341773,0.0498004118748,0.049772806325,0.0506009728196,0.0507942116683,0.0509322394174,0.0510150560669,0.0513187171149,0.0520916725098,0.0531682889528,0.0532235000525,0.0534167389012,0.0534719500008,0.053140683403,0.0533063167019,0.0543553275951,0.054824621942,0.054824621942,0.0551558885398,0.0549074385915,0.0554595495878,0.0560116605842,0.0567017993297,0.0573091214258,0.05819249902,0.0585789767175,0.0580820768207,0.0587722155662,0.0594071432121,0.0593243265626,0.0594899598615,0.0591862988135,0.0591310877139,0.0596003820608,0.0603457319059,0.0605665763045,0.0616707982973,0.0614499538987,0.0606769985038,0.0612015039504,0.0608978429023,0.0621400926442,0.0624161481424,0.0630510757883,0.0628026258399,0.0630786813381,0.0628026258399,0.0638792422829,0.0649558587258,0.065231914224,0.0664741639659,0.0660324751688,0.0655631808219,0.0655355752721,0.065397547523,0.0656736030212,0.0665569806154,0.0671919082612,0.0670262749623,0.0668054305638,0.0679372581064,0.0689586634497,0.0701733076418,0.0706426019887,0.0715259795829,0.0722989349779,0.0722161183284,0.0729062570739,0.073817240218,0.0748662511111,0.0751147010595,0.0753631510079,0.0760808953032,0.0755839954064,0.0756392065061,0.0749766733104,0.0753907565577,0.0748110400115,0.0761913175025,0.0769090617978,0.0766882173992,0.077185117296,0.0771299061963,0.0790070835841,0.0804149666249,0.081933271865,0.0835619993043,0.0848594601459,0.0852459378433,0.0862949487365,0.0869574819322,0.0882549427737,0.0898560646632,0.0902149368109,0.091208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m <- 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ycorr <- 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altd  <- c(215)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('A549-100nM-Dex-3h-p300.pooled.sorted.pseudoRep1.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) : 215',bty='n')
dev.off()