# R script for Peak Model
#  -- generated by MACS
p <- c(0.0457537165128,0.054088359369,0.0613377622699,0.0688910323584,0.0764443024468,0.0751420145005,0.0757931584737,0.0770086272235,0.0756629296791,0.0773993136074,0.0771388560182,0.0765745312415,0.0770086272235,0.0780938671788,0.0780070479824,0.0803945758839,0.0802643470893,0.0793961551251,0.0793527455269,0.0765311216432,0.0770520368218,0.0767915792325,0.0775729520003,0.0762272544558,0.0753590624916,0.0728847153937,0.0727978961972,0.0742738225364,0.0757497488755,0.0771388560182,0.0782675055716,0.0793527455269,0.0784411439645,0.0787450111519,0.0808720814642,0.0804813950803,0.0804813950803,0.0797434319107,0.0807418526696,0.0798302511072,0.0793093359286,0.0798736607054,0.0806984430714,0.0798302511072,0.0777031807949,0.0797000223125,0.0788318303483,0.0793093359286,0.0770520368218,0.0765745312415,0.0759667968665,0.073362220974,0.0736226785632,0.0753590624916,0.0754024720898,0.0738397265543,0.0731017633847,0.0717994754384,0.0728413057954,0.0732754017775,0.0729281249919,0.073579268965,0.0721901618223,0.0711917410635,0.073362220974,0.0743606417328,0.0750551953041,0.0756629296791,0.0760970256611,0.0753156528934,0.0756629296791,0.0767481696343,0.0774427232056,0.0774861328039,0.0770086272235,0.0775295424021,0.0778334095895,0.0777031807949,0.0785279631609,0.0793093359286,0.0789186495448,0.0792225167322,0.0800472990982,0.0800038895,0.0806116238749,0.0795263839197,0.0804813950803,0.0812193582499,0.079179107134,0.0800472990982,0.0806116238749,0.0806984430714,0.0809589006606,0.0814798158391,0.0799604799018,0.0799604799018,0.0800038895,0.0793093359286,0.0803511662857,0.0800907086964,0.0802643470893,0.0795697935179,0.0777465903931,0.0768783984289,0.0767915792325,0.0784845535627,0.0779636383842,0.0794829743215,0.0793527455269,0.0785279631609,0.0779202287859,0.0776163615985,0.0782675055716,0.0789186495448,0.0797000223125,0.078137276777,0.0778334095895,0.075228833697,0.0765745312415,0.0768349888307,0.0762272544558,0.0750117857059,0.075445881688,0.0763574832504,0.0767047600361,0.07709544642,0.0771388560182,0.0785713727591,0.0768783984289,0.0767481696343,0.0777899999913,0.078137276777,0.0769218080271,0.0753590624916,0.0748815569113,0.073579268965,0.0742738225364,0.0740567745453,0.0746645089202,0.075228833697,0.0761404352594,0.0774861328039,0.0796132031161,0.0795263839197,0.0789186495448,0.0798736607054,0.0780938671788,0.0777465903931,0.0778334095895,0.0787884207501,0.0780504575806,0.0772690848128,0.0762272544558,0.0757931584737,0.0762272544558,0.07709544642,0.0788752399466,0.0806550334731,0.0797434319107,0.0779636383842,0.0772256752146,0.0778334095895,0.0768349888307,0.0779636383842,0.0776163615985,0.0764443024468,0.0756195200808,0.0741870033399,0.0732754017775,0.0737094977596,0.0745342801256,0.0750117857059,0.0752722432952,0.0752722432952,0.0753156528934,0.0755327008844,0.0753156528934,0.0753590624916,0.077312494411,0.0788752399466,0.0786147823573,0.0778334095895,0.0774861328039,0.0766613504379,0.0762272544558,0.0759233872683,0.0757931584737,0.0758799776701,0.0753590624916,0.0751854240988,0.0751854240988,0.076270664054,0.0777031807949,0.0787450111519,0.079786841509,0.0806984430714,0.0821309598123,0.0829557421782,0.0821743694105,0.0807852622678,0.0805682142767,0.0807418526696,0.0801341182946,0.0799604799018,0.0790054687412,0.0782240959734,0.0768349888307,0.0758799776701,0.0769218080271,0.076270664054,0.0763140736522,0.0747513281167,0.0747513281167,0.075228833697,0.0768783984289,0.07709544642,0.0774427232056,0.0783977343663,0.0782240959734,0.0806116238749,0.0827386941872,0.0825216461961,0.0831293805711,0.0824782365979,0.0810023102588,0.0808720814642,0.0813061774463,0.0809589006606,0.0808720814642,0.0793093359286,0.0783977343663,0.0792659263304,0.0796132031161,0.0805248046785,0.0817402734284,0.0828689229818,0.0833464285621,0.0833898381603,0.0829557421782,0.0848223549012,0.0830859709729,0.0831727901693,0.0831727901693,0.0834332477585,0.0818270926248,0.0813929966427,0.0809154910624,0.0803511662857,0.0813061774463,0.079179107134,0.0801341182946,0.0804813950803,0.0790054687412,0.0774861328039,0.0771822656164,0.0763574832504,0.0757931584737,0.0748815569113,0.0736226785632,0.0748815569113,0.0751854240988,0.0757063392773,0.0760102064647,0.0770086272235,0.0775295424021,0.0780938671788,0.0787450111519,0.0798302511072,0.0808720814642,0.0803511662857,0.0799170703036,0.0803945758839,0.0801775278928,0.0791356975358,0.0801775278928,0.0799170703036,0.0790922879376,0.0795697935179,0.0805248046785,0.0796132031161,0.0797000223125,0.0773559040092,0.0781806863752,0.0794395647233,0.0783109151698,0.0800038895,0.0796132031161,0.0798736607054,0.0785713727591,0.0795263839197,0.0809589006606,0.0814364062409,0.0819139118212,0.0812193582499,0.0828689229818,0.0822177790087,0.0846921261066,0.0838239341424,0.0846053069102,0.0846487165084,0.0839107533388,0.0855603180708,0.0857773660619,0.0859944140529,0.085603727669,0.0859944140529,0.0862114620439,0.0869060156153,0.0867323772225,0.0880346651687,0.0881648939634,0.0861246428475,0.0846053069102,0.0847355357048,0.08469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m <- 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ycorr <- 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altd  <- c(4, 189, 212, 523, 563, 588)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('FigS2C_WT_Smc3HA_IP-GSM2813883/all.1x36mers.unique.MACS2.1.0_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) : 4,189,212,523,563,588',bty='n')
dev.off()