# R script for Peak Model
#  -- generated by MACS
p <- c(0.0195746832976,0.0232711900147,0.0261275815689,0.0294880422208,0.0324284452913,0.0328485028728,0.0328485028728,0.0338566410684,0.0339406525847,0.034612744715,0.0343607101661,0.0337726295521,0.0347807677476,0.0356208829106,0.036292975041,0.036292975041,0.0372171017203,0.0358729174595,0.0362089635247,0.0366290211062,0.0384772744648,0.0397374472093,0.0408295969211,0.0403255278234,0.0404095393397,0.0400734932745,0.0399894817582,0.0399894817582,0.0398214587256,0.0384772744648,0.0374691362692,0.0368810556551,0.035452859878,0.035452859878,0.0345287331987,0.0345287331987,0.0327644913565,0.0336046065195,0.0321764107424,0.0326804798402,0.0325964683239,0.0322604222587,0.0319243761935,0.0320923992261,0.0326804798402,0.0337726295521,0.034612744715,0.0353688483617,0.0367130326225,0.0380572168833,0.0383092514322,0.0387293090137,0.0403255278234,0.0399054702419,0.0403255278234,0.0391493665952,0.0391493665952,0.0382252399159,0.037973205367,0.0363769865573,0.0369650671714,0.0363769865573,0.0365450095899,0.0368810556551,0.037133090204,0.0373011132366,0.0372171017203,0.0381412283996,0.0383932629485,0.039653435693,0.0393173896278,0.039653435693,0.0377211708181,0.037973205367,0.0377211708181,0.0384772744648,0.0387293090137,0.0377211708181,0.0377211708181,0.0373851247529,0.0373851247529,0.0372171017203,0.0370490786877,0.0374691362692,0.0377211708181,0.0382252399159,0.037973205367,0.0388973320463,0.0388973320463,0.0393173896278,0.03881332053,0.0388973320463,0.0395694241767,0.0391493665952,0.0389813435626,0.0383932629485,0.0398214587256,0.0399894817582,0.040493550856,0.0400734932745,0.0406615738885,0.0417537236004,0.043601976959,0.0431819193775,0.0440220345405,0.0446101151546,0.044442092122,0.044442092122,0.0453662188013,0.0457022648665,0.0466263915458,0.0466263915458,0.0457022648665,0.0468784260946,0.0474665067087,0.0474665067087,0.0474665067087,0.0473824951924,0.0468784260946,0.0467944145784,0.0457862763828,0.0448621497035,0.0453662188013,0.0449461612198,0.0448621497035,0.0441900575731,0.0436859884753,0.0436859884753,0.0435179654427,0.0421737811819,0.0423418042145,0.0425938387634,0.0417537236004,0.0420897696656,0.0411656429863,0.0409136084374,0.0418377351167,0.0418377351167,0.0409136084374,0.0431819193775,0.0432659308938,0.0434339539264,0.0432659308938,0.0429298848286,0.0429298848286,0.0433499424101,0.0428458733123,0.0437699999916,0.0435179654427,0.0430138963449,0.0432659308938,0.0435179654427,0.0448621497035,0.0446101151546,0.0445261036383,0.0454502303176,0.0458702878991,0.0448621497035,0.0472144721598,0.0474665067087,0.0477185412576,0.0472984836761,0.0457022648665,0.0466263915458,0.0467104030621,0.0451981957687,0.0449461612198,0.0450301727361,0.0443580806057,0.0453662188013,0.0449461612198,0.0457862763828,0.047550518225,0.0476345297413,0.0481385988391,0.049230748551,0.0497348176488,0.0506589443281,0.0503228982629,0.0494827830999,0.0501548752303,0.0516670825237,0.0510790019096,0.0509949903933,0.0514990594911,0.0520031285889,0.0525071976867,0.0519191170726,0.053179289817,0.053179289817,0.0535153358822,0.0524231861704,0.0528432437519,0.0528432437519,0.0530952783007,0.0535153358822,0.0535153358822,0.0542714395289,0.053179289817,0.0543554510452,0.0541034164963,0.0553635892408,0.0551955662082,0.0561196928875,0.0562877159201,0.0559516698549,0.0551955662082,0.0558676583386,0.0569598080505,0.0572118425994,0.0576319001809,0.0561196928875,0.0566237619853,0.0570438195668,0.0570438195668,0.0569598080505,0.0584720153439,0.0579679462461,0.0578839347298,0.0570438195668,0.0562037044038,0.0568757965342,0.0569598080505,0.0557836468223,0.0560356813712,0.0572958541157,0.0564557389527,0.0556156237897,0.0563717274364,0.0564557389527,0.057379865632,0.0576319001809,0.0577159116972,0.0589760844417,0.059060095958,0.0575478886646,0.0597321880883,0.0615804414469,0.0608243378002,0.0607403262839,0.0617484644795,0.0625045681262,0.0626725911588,0.0620845105447,0.0628406141914,0.0641007869359,0.0622525335773,0.0615804414469,0.0618324759958,0.0629246257077,0.0623365450936,0.0624205566099,0.0629246257077,0.063008637224,0.0628406141914,0.063008637224,0.0644368330011,0.0654449711967,0.0658650287781,0.066117063327,0.065528982713,0.0647728790663,0.0649409020989,0.0641007869359,0.0626725911588,0.0644368330011,0.0642688099685,0.0635127063218,0.0641007869359,0.0636807293544,0.0639327639033,0.0641847984522,0.0645208445174,0.0659490402944,0.06695717849,0.0648568905826,0.063848752387,0.0645208445174,0.0637647408707,0.0644368330011,0.0648568905826,0.0649409020989,0.0659490402944,0.066117063327,0.0664531093922,0.0672932245552,0.0695615354953,0.0685533972997,0.0689734548812,0.0692254894301,0.071157754305,0.0722499040168,0.0718298464353,0.0724179270494,0.072585950082,0.0714097888539,0.071157754305,0.0718298464353,0.0718298464353,0.0718298464353,0.0692254894301,0.068637408816,0.0682173512345,0.0684693857834,0.0693935124627,0.070317639142,0.0700656045931,0.0695615354953,0.0702336276257,0.0708217082398,0.0723339155331,0.0732580422124,0.0746022264732,0.0761984452829,0.0769545489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m <- 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ycorr <- 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altd  <- c(72)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('SWI4_rep1-GSM5884447.2x25mers.Spar+sacCer3.unique.dedup.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) : 72',bty='n')
dev.off()