# R script for Peak Model
#  -- generated by MACS
p <- c(0.0152468162714,0.0178104402462,0.0200142573474,0.0228477364774,0.0256362397483,0.0254113604523,0.0255912638891,0.025996046622,0.0264008293548,0.0265582448621,0.0260410224812,0.0256812156075,0.0260410224812,0.0261759500588,0.0258161431851,0.025996046622,0.0261759500588,0.0257037035371,0.0255687759595,0.0250965294378,0.0253888725227,0.0259060949036,0.0256362397483,0.0252539449451,0.0250515535786,0.0255238001003,0.0252539449451,0.0256587276779,0.0255687759595,0.0259285828332,0.02610848627,0.0260410224812,0.02610848627,0.026333365566,0.0266931724397,0.0267606362285,0.0272778586094,0.0273678103278,0.027412786187,0.0277276172015,0.0277950809903,0.0277051292719,0.0279075206383,0.0275477137646,0.0272553706798,0.0269855155245,0.0264008293548,0.0261534621292,0.026333365566,0.0262883897068,0.0258611190444,0.0255013121707,0.0254113604523,0.0259510707628,0.0260859983404,0.0257711673259,0.0257037035371,0.0257936552555,0.025883606974,0.0255687759595,0.0257037035371,0.025996046622,0.0260635104108,0.0254338483819,0.0256812156075,0.0257486793963,0.0259060949036,0.0255013121707,0.0249840897898,0.025141505297,0.0256137518187,0.0257261914667,0.0258386311147,0.0262434138476,0.0266706845101,0.027187906891,0.0272328827502,0.0277950809903,0.0278850327087,0.0276151775534,0.0273678103278,0.0279974723567,0.0278850327087,0.0273678103278,0.0269630275949,0.0263783414252,0.0261534621292,0.0257711673259,0.0264907810733,0.0271429310318,0.0270080034541,0.0269855155245,0.0267381482989,0.0267831241581,0.0265357569325,0.0269630275949,0.0272553706798,0.0277725930607,0.0274577620462,0.0275027379054,0.0276601534127,0.027412786187,0.0275027379054,0.0285596705968,0.0283123033712,0.0281099120047,0.0277950809903,0.0276601534127,0.0279300085679,0.0275926896238,0.0279075206383,0.0281099120047,0.0281773757935,0.027525225835,0.0280874240751,0.0278850327087,0.0279749844271,0.0279524964975,0.0282448395824,0.0280424482159,0.0279300085679,0.0272103948206,0.0274802499758,0.0269630275949,0.027075467243,0.027300346539,0.0276826413423,0.0281548878639,0.0275926896238,0.0275702016942,0.0273453223982,0.0277276172015,0.0278625447791,0.0283572792304,0.028604646456,0.0288745016113,0.0287620619632,0.0286271343856,0.0285821585264,0.0289644533297,0.0291218688369,0.0292118205553,0.0289419654001,0.0293917239921,0.0293692360625,0.0293467481329,0.0294816757106,0.0291443567665,0.0291668446961,0.0290094291889,0.0290319171185,0.0288745016113,0.0290993809073,0.028492206808,0.0281998637231,0.028604646456,0.0285821585264,0.0287620619632,0.0291218688369,0.0292792843441,0.0291443567665,0.0291893326257,0.0291218688369,0.0296615791474,0.0297515308658,0.0291443567665,0.0294142119218,0.0296615791474,0.0300438739507,0.0300663618803,0.0302687532467,0.0300438739507,0.0302462653171,0.0304036808243,0.0303811928947,0.0303362170355,0.0299314343026,0.0296615791474,0.0290768929777,0.0295491394994,0.0293242602033,0.0293692360625,0.0295266515698,0.0288070378224,0.0295266515698,0.0298414825842,0.0301113377395,0.0301788015283,0.0302912411763,0.0301113377395,0.0306735359796,0.0306735359796,0.0306960239092,0.0310783187124,0.0306960239092,0.0308984152756,0.0308984152756,0.030988366994,0.0309658790644,0.0305835842611,0.0303587049651,0.0311232945716,0.0306960239092,0.0305835842611,0.0306060721908,0.0306285601204,0.0305610963315,0.0309209032052,0.0312357342197,0.0317304686709,0.0324950582775,0.0323601306998,0.0326749617143,0.0331247203064,0.0331247203064,0.0335295030392,0.0337094064761,0.0337318944057,0.0336194547577,0.0341591650681,0.0339792616313,0.0341366771385,0.0343840443642,0.0347438512378,0.0349237546747,0.0345864357306,0.0352160977595,0.0352835615483,0.035530928774,0.0348562908859,0.0345189719418,0.0347438512378,0.0352835615483,0.0349462426043,0.0352385856891,0.0355983925628,0.0351711219003,0.0349462426043,0.0353735132668,0.0360031752957,0.0363854700989,0.0364079580285,0.0364754218173,0.0371500597055,0.0370825959166,0.0374873786495,0.0378246975936,0.0378921613824,0.03802708896,0.0381170406784,0.0383868958337,0.0388141664961,0.0387691906369,0.0393988526658,0.039443828525,0.0396237319619,0.0398261233283,0.04029836985,0.0404332974276,0.0409954956677,0.0408155922309,0.0405682250052,0.0408155922309,0.0403658336388,0.0403658336388,0.0400060267651,0.0399610509059,0.0398935871171,0.0402309060612,0.0393988526658,0.0397361716099,0.0403208577796,0.0408155922309,0.0406581767236,0.041490230119,0.0418500369926,0.0424347231623,0.0433567282761,0.0431768248393,0.0442337575306,0.0449083954188,0.0454930815885,0.0453581540108,0.0459878160397,0.0460777677582,0.046145231547,0.0459653281101,0.0458304005325,0.0467748935759,0.0468423573647,0.0469547970127,0.0459878160397,0.0467299177167,0.0481016814225,0.0478093383376,0.0483940245073,0.0491586141139,0.0498557399316,0.0498782278612,0.0503729623125,0.050912672623,0.0523069242584,0.0526217552729,0.0521944846104,0.0528016587097,0.0530940017945,0.0531614655833,0.0528691224985,0.053296393161,0.0541959103451,0.0547581085852,0.0545782051484,0.0546456689372,0.0550504516701,0.056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m <- 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ycorr <- 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altd  <- c(174)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('ChIP-Seq_Sox2_V65-GSM1082341.36mers.mm10.unique.MACS2_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) : 174',bty='n')
dev.off()