# R script for Peak Model
#  -- generated by MACS
p <- c(0.03563520576233164,0.0419074066346228,0.0480700125991992,0.05422418818625908,0.060664996608880646,0.060833604159211054,0.06092633831189278,0.06159233813569789,0.06189583172629262,0.0618874013487761,0.06125512303503707,0.06116238888235535,0.061128667372289267,0.06074930038404585,0.060302490375670266,0.060698718118946726,0.060732439629012806,0.06061441434378152,0.0605216801910998,0.06021818660050506,0.060842034536727575,0.060724009251496285,0.06098535095450842,0.06159233813569789,0.06167664191086309,0.061263553412553594,0.061153958504838825,0.060909477556859735,0.060976920576991896,0.06156704700314832,0.0613478571877188,0.0618452494611935,0.06178623681857785,0.0613478571877188,0.06144902171791704,0.06154175587059876,0.062115021541722146,0.06217403418433779,0.06191269248132566,0.06169350266589613,0.06194641399139174,0.06142373058536748,0.06113709774980579,0.061398439452817914,0.06149960398301616,0.06178623681857785,0.06121297114745447,0.06100221170954146,0.06153332549308224,0.06210659116420563,0.06178623681857785,0.06191269248132566,0.06203071776655694,0.0618874013487761,0.061440591340400516,0.06106965472967362,0.06107808510719014,0.06157547738066484,0.06116238888235535,0.06037836377331895,0.060479528303517195,0.06003271829514162,0.06042051566090155,0.060260338488087664,0.060504819436066754,0.060698718118946726,0.06132256605516923,0.06101064208705798,0.061128667372289267,0.06154175587059876,0.06171879379844569,0.062410084754800366,0.06205600889910651,0.06262927457022989,0.0628821858957255,0.06280631249807682,0.062367932867217764,0.0627978821205603,0.06311823646618807,0.06320254024135327,0.06326998326148545,0.06298335042592375,0.06323626175141936,0.06326998326148545,0.06311823646618807,0.0632531225064524,0.06364935024972886,0.06341329967926629,0.06332056552658456,0.06340486930174977,0.06304236306853939,0.06289904665075854,0.06290747702827507,0.06250281890748209,0.062435375887349924,0.06217403418433779,0.06150803436053268,0.06175251530851177,0.0613900090753014,0.06150803436053268,0.061651350778313525,0.061769376063544816,0.061609198890730923,0.06165978115583005,0.06185367983871002,0.061904262103809136,0.06231735060211864,0.06239322399976732,0.06251124928499861,0.06202228738904043,0.06217403418433779,0.06230892022460212,0.06202228738904043,0.06203071776655694,0.06202228738904043,0.06174408493099525,0.06170193304341265,0.06156704700314832,0.061904262103809136,0.06175251530851177,0.06230892022460212,0.062233046826953436,0.062401654377283844,0.062401654377283844,0.062224616449436915,0.06291590740579159,0.06273886947794466,0.06255340117258121,0.06203071776655694,0.06285689476317594,0.06224990758198647,0.06278102136552725,0.06289061627324202,0.06343859081181585,0.06354818571953061,0.06347231232188193,0.06391069195274099,0.06357347685208017,0.06418889441078617,0.06347231232188193,0.06343016043429933,0.06302550231350636,0.06311823646618807,0.06290747702827507,0.06309294533363852,0.06327841363900197,0.06278102136552725,0.06305922382357243,0.06310980608867156,0.06360719836214626,0.06414674252320356,0.06414674252320356,0.06415517290072008,0.06418046403326964,0.06398656535038967,0.06369993251482799,0.06402028686045576,0.0639612742178401,0.06354818571953061,0.0632531225064524,0.06295805929337418,0.06294962891585766,0.06273886947794466,0.062233046826953436,0.0623847936222508,0.06212345191923867,0.06209816078668911,0.06256183155009773,0.06272200872291162,0.06274729985546118,0.062443806264866446,0.06252811004003164,0.06286532514069246,0.06324469212893588,0.06321940099638632,0.06345545156684888,0.06372522364737754,0.06367464138227842,0.06389383119770795,0.06396970459535663,0.06435750196111657,0.06458512215406262,0.06454297026648002,0.06470314743929391,0.06454297026648002,0.06465256517419478,0.06440808422621569,0.06472000819432695,0.06478745121445911,0.065158387825186,0.06523426122283468,0.06520897009028513,0.06547874217081379,0.06522583084531818,0.06493919800975648,0.06498134989733907,0.06493076763223996,0.06454297026648002,0.06426476780843485,0.0641636032782366,0.06385167931012535,0.06390226157522447,0.0636662110047619,0.06405400837052183,0.06470314743929391,0.0646609955517113,0.06500664102988864,0.06478745121445911,0.06477902083694259,0.06450081837889741,0.06500664102988864,0.06467785630674434,0.06509094480505384,0.06497291951982256,0.06504036253995472,0.06531013462048338,0.06539443839564858,0.06579909651644156,0.06582438764899111,0.06646509634024667,0.06648195709527971,0.06686132408352312,0.06658312162547796,0.0667685899308414,0.06701307087882048,0.06728284295934914,0.06724912144928306,0.06703836201137005,0.06758633654994388,0.06749360239726215,0.06720696956170046,0.06748517201974563,0.0676790707026256,0.06835350090394723,0.06819332373113335,0.06794884278315425,0.06807529844590206,0.06862327298447587,0.06893519695258714,0.06910380450291755,0.0694157284710288,0.06944944998109488,0.06963491828645833,0.06982881696933829,0.07071400660857294,0.07139686718741109,0.07170036077800582,0.07184367719578666,0.07162448738035714,0.07169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m <- 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ycorr <- 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altd  <- c(193)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('GRCh38.p13-GSM733718_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) : 193',bty='n')
dev.off()