# R script for Peak Model
#  -- generated by MACS
p <- c(0.0393215957422,0.0457428039501,0.0521409038964,0.0585996630296,0.0653443869007,0.0654483740782,0.0654888135361,0.0655234759285,0.0657054534891,0.0656245745733,0.065696787891,0.0658123291993,0.0660954054046,0.0663351536192,0.0661098480681,0.0662542747034,0.0661965040493,0.0663727045444,0.0663293765538,0.0663351536192,0.066080962741,0.0662340549745,0.0657690012086,0.0657776668068,0.0658932081151,0.0658932081151,0.0657776668068,0.0658412145263,0.0659798640963,0.0660665200775,0.0661936155166,0.0661242907316,0.0666095642264,0.0665517935723,0.0666702234133,0.0667684335253,0.0668059844505,0.066603787161,0.0667193284693,0.0666124527591,0.0667279940674,0.0671410542445,0.067481901104,0.0676234392066,0.0677129837205,0.0676552130664,0.0681260438977,0.068458225159,0.0682531393368,0.0686517568504,0.0689261674575,0.0685362155421,0.0682155884116,0.0681635948229,0.0680480535146,0.0680076140567,0.0677707543747,0.0675887768141,0.0676205506739,0.0674559043096,0.0670399555998,0.0672681496836,0.0673201432724,0.0672797038145,0.067461681375,0.0678111938326,0.0678400791597,0.0679758401969,0.0683253526545,0.0684437824955,0.068645979785,0.0683686806451,0.0682820246639,0.0680018369913,0.0679065154119,0.0675483373562,0.0672594840855,0.0670861721231,0.0669417454877,0.0666846660768,0.0666442266189,0.0667857647216,0.0668435353757,0.0673259203378,0.0672537070201,0.0675396717581,0.0678314135615,0.0680422764492,0.0679700631315,0.0682184769443,0.0681809260191,0.0680249452529,0.0679787287296,0.0679671745988,0.0679989484586,0.0677851970382,0.0678140823653,0.0675743341506,0.0678545218232,0.0676465474683,0.0678343020942,0.068221365477,0.0684148971684,0.0683109099909,0.0683744577105,0.0686113173925,0.0686199829906,0.0686113173925,0.0683426838507,0.0685997632616,0.0689723839809,0.0688164032147,0.0687095275045,0.068842400009,0.068862619738,0.0687008619064,0.0686633109812,0.0687817408222,0.0686661995139,0.0685737664673,0.0681578177574,0.0681751489537,0.0682762475984,0.0680942700379,0.0680971585706,0.068319575589,0.0685159958131,0.0686113173925,0.0687846293549,0.0688712853361,0.0692958996441,0.0694952084008,0.0697060712885,0.0698216125968,0.0703473255495,0.0702346727739,0.0701855677179,0.0701480167927,0.0701855677179,0.0706823953435,0.0705408572408,0.070835487577,0.0706881724089,0.0708123793153,0.070598627895,0.0708412646424,0.0709596944834,0.0712485477541,0.0715460666229,0.0710694587262,0.0712658789503,0.0711878885672,0.0714276367819,0.0714738533052,0.0715402895575,0.0715662863519,0.0717742607068,0.0717193785853,0.0714334138473,0.0713554234642,0.0713583119969,0.0714998500996,0.071644276735,0.0720631139775,0.0721006649027,0.072531056276,0.0725368333415,0.0726234893227,0.0729210081915,0.0733716192938,0.0734033931536,0.0734120587517,0.0730654348269,0.0730943201539,0.0732560779855,0.072935450855,0.0728690146028,0.0731376481445,0.0732243041258,0.0731260940137,0.0730307724344,0.0731174284156,0.0734033931536,0.0733860619574,0.0735304885927,0.0739724340969,0.0740533130127,0.0739666570315,0.0739984308913,0.0742786185639,0.0746165768906,0.0747783347222,0.0748794333669,0.0749343154884,0.0747667805914,0.0747234526008,0.0751827293012,0.0754773596373,0.0757344390482,0.0758990854126,0.075904862478,0.0760319579171,0.0761186138983,0.0764190212998,0.0766212185893,0.0762457093374,0.0758124294313,0.0758095408986,0.0759799643284,0.0762543749355,0.0765605594025,0.0765172314119,0.0766732121781,0.0766529924491,0.0769649539815,0.0776582018312,0.0781521409241,0.0781030358681,0.0781030358681,0.0779499436346,0.0781376982606,0.078192580382,0.0782532395689,0.078192580382,0.0779470551019,0.0775657687846,0.0778690647188,0.0780683734756,0.0783196758211,0.0787673983907,0.0786807424095,0.0792700030818,0.0795559678198,0.0798563752213,0.0801481170247,0.0806738299774,0.0805062950804,0.0809511291173,0.0808702502015,0.0809684603136,0.080835587809,0.0808182566128,0.0811937658647,0.0814190714159,0.08161549164,0.0818667939855,0.0820892110039,0.0825051597138,0.0827506849939,0.082354956013,0.0825658189006,0.0825080482465,0.0823693986765,0.0823722872092,0.0826235895548,0.082453166125,0.0822798541626,0.0817368100137,0.0818783481163,0.0822914082934,0.0824098381344,0.0822191949758,0.0820949880693,0.0821527587235,0.0821527587235,0.0823867298728,0.0827882359191,0.0830626465262,0.0834352672455,0.0836201333387,0.084070744441,0.084593568861,0.085047068496,0.0850817308885,0.0854254662807,0.0856854342243,0.0858905200465,0.0861909274481,0.0864566724571,0.0866270958868,0.086733971597,0.0867368601297,0.0870574872602,0.0875398722223,0.0877767319043,0.0878864961471,0.0878633878855,0.0880944705021,0.0880135915863,0.0878056172313,0.0879442668013,0.0881897920814,0.0882880021934,0.0884555370904,0.0881580182216,0.0884295402961,0.0884757568194,0.0887241706322,0.0888281578097,0.089327873968,0.0896889405564,0.0901424401914,0.090777917387,0.091112987181,0.0919824355259,0.0927478966932,0.0936260106362,0.0943856947382,0.0950327260646,0.0960090501196,0.096725406231,0.0973522178284,0.0978143830616,0.0985971754252,0.0989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m <- 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ycorr <- 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altd  <- c(294)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('Monodelphis_domestica-male-liver-H3K4me3-ERR572135.50mers.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) : 294',bty='n')
dev.off()