# R script for Peak Model
#  -- generated by MACS
p <- c(0.0379802670361,0.0444859469786,0.0508195758813,0.0574542941036,0.0637018974864,0.0634868336866,0.0636696379164,0.0638309357662,0.0638309357662,0.0637986761963,0.0639922336161,0.0639707272361,0.0638416889562,0.0636803911064,0.0638739485262,0.0638524421462,0.0635728592065,0.0634545741167,0.063196497557,0.0637341570564,0.0635190932566,0.0636696379164,0.0641105187059,0.064056752756,0.0644116080256,0.0646911909653,0.0648202292451,0.0650890589948,0.0656159653042,0.0650675526148,0.0651965908947,0.064927761145,0.0649815270949,0.0648309824351,0.0646159186353,0.0645298931154,0.0646481782053,0.0644223612156,0.0644008548356,0.0645406463054,0.0644868803555,0.0645083867355,0.0642503101758,0.0645836590654,0.0645406463054,0.0651965908947,0.0651643313247,0.0656912376341,0.0656159653042,0.065777263154,0.0658525354839,0.0664224545533,0.0668525821528,0.0670461395725,0.0671859310424,0.0669278544827,0.0673902416521,0.0671321650924,0.0673364757022,0.0672504501823,0.0677128373518,0.0676268118319,0.067497773552,0.0672719565623,0.0669816204326,0.0671321650924,0.0667988162028,0.0674332544121,0.0674332544121,0.0678418756316,0.0677558501117,0.0676053054519,0.0677235905418,0.0678526288216,0.0684333010809,0.0685838457408,0.0689494542003,0.0687666499705,0.0685515861708,0.0689064414404,0.0690032201503,0.0689924669603,0.0686591180707,0.0684548074609,0.0685408329808,0.0681967309012,0.068347275561,0.0684870670309,0.06928280309,0.0690677392902,0.0689171946304,0.0691107520501,0.0696269051696,0.0697882030194,0.0698957349192,0.0701968242389,0.0699279944892,0.0700570327691,0.0698312157793,0.0699172412992,0.0699172412992,0.0698419689693,0.0698634753493,0.0702720965688,0.0703688752787,0.0706377050284,0.0710785858179,0.0710570794379,0.070981807108,0.0710678326279,0.0715839857473,0.071799049547,0.0717345304071,0.0718958282569,0.0719926069668,0.0720678792967,0.0715624793673,0.0713904283275,0.0713689219475,0.0713689219475,0.0711323517678,0.0713044028076,0.0714549474674,0.0711323517678,0.0711968709077,0.070971053918,0.0711646113378,0.0712506368577,0.0716700112672,0.0717345304071,0.0716269985072,0.0714979602274,0.0715624793673,0.0720033601568,0.0717882963571,0.0721001388667,0.0725517728462,0.0730894323456,0.0732077174354,0.073584079085,0.0738851684046,0.0740034534945,0.0740034534945,0.0738529088347,0.0740572194444,0.0741217385844,0.0741647513443,0.0740679726344,0.0741539981543,0.0740787258244,0.0738744152146,0.0741755045343,0.0743368023841,0.0746593980837,0.0748744618835,0.0747561767936,0.0747346704137,0.0746163853238,0.0747669299836,0.0745733725638,0.0749712405934,0.0748529555035,0.0750465129233,0.0755304064727,0.0757024575125,0.0758530021724,0.0760573127821,0.076132585112,0.0762078574419,0.0765412063316,0.0765196999516,0.0768207892712,0.0767562701313,0.0762616233919,0.0762831297719,0.0765734659015,0.0768422956512,0.077003593501,0.0771433849709,0.0770896190209,0.0773584487706,0.0772509168707,0.0774874870505,0.0779821337899,0.0781756912097,0.0778100827501,0.0774874870505,0.0775304998104,0.0775304998104,0.07785309551,0.0778423423201,0.0783154826795,0.0784660273393,0.0783477422495,0.0782724699196,0.078745610279,0.0789284145088,0.0794338144382,0.079584359098,0.079584359098,0.079638125048,0.0792402570184,0.0794230612482,0.0795628527181,0.0793047761584,0.0791972442585,0.0793370357283,0.0794768271982,0.0798854484177,0.0802080441173,0.0803908483471,0.0807457036167,0.0806704312868,0.0810252865564,0.0816274651957,0.0819930736553,0.0822834097849,0.0821328651251,0.0818962949454,0.0818747885654,0.0820038268453,0.0823586821148,0.0827888097143,0.0829501075642,0.0826812778145,0.0831651713639,0.0833157160237,0.0836275585334,0.0837781031932,0.0837135840533,0.0842082307927,0.0842189839827,0.0843480222625,0.0845200733023,0.0852405370315,0.0850362264217,0.0851222519416,0.0851867710816,0.0854663540213,0.085702924201,0.0853480689314,0.0856276518711,0.0861007922305,0.0859502475707,0.0861653113704,0.0860362730906,0.0867244772498,0.0870470729494,0.0870470729494,0.0869610474295,0.0875524728788,0.0876277452088,0.0876922643487,0.0877890430586,0.0875524728788,0.0881223919482,0.0882084174681,0.0879718472884,0.0886708046375,0.0892622300869,0.0896063321665,0.090047212956,0.0898106427762,0.0904020682255,0.0908106894451,0.0905956256453,0.0905956256453,0.090918221345,0.0908106894451,0.0911332851447,0.0912193106646,0.0913268425645,0.0915741659342,0.0914558808443,0.0914236212744,0.0924129147532,0.092584965793,0.0929398210626,0.0927677700228,0.0928645487327,0.0927355104529,0.0927247572629,0.0931441316724,0.0931441316724,0.0935419997019,0.0931011189124,0.0930258465825,0.0928107827828,0.0931441316724,0.0932839231422,0.093498986942,0.0937893230716,0.0936495316018,0.0939183613515,0.0940581528213,0.0946925910306,0.0952517569099,0.0955420930396,0.0960259865891,0.0963593354787,0.0970260332579,0.0973593821475,0.097843275697,0.0981336118266,0.0984454543363,0.0984884670962,0.098639011756,0.0992734499653,0.0990153734056,0.0990691393555,0.098660518136,0.0985422330461,0.0985637394261,0.0988003096058,0.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m <- 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ycorr <- 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altd  <- c(244)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('S2-AbdA_HA-AbdA_ChIPSeq_Rep2-GSM2706046.36mers.unique.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) : 244',bty='n')
dev.off()