# R script for Peak Model
#  -- generated by MACS
p <- c(0.0402242818899,0.0468019171892,0.0536560516198,0.0599521144092,0.066562726669,0.0665931669404,0.0664384288944,0.0665145295727,0.0662025167915,0.0659412377958,0.0656495185288,0.0654897071042,0.0650533965483,0.0654186798044,0.0654846337257,0.0654465833865,0.0657712796141,0.0655379042005,0.0657256192071,0.0655023905506,0.0655505876469,0.0656545919073,0.0656951789358,0.0657459127213,0.0656824954894,0.0656495185288,0.0655962480539,0.065578491229,0.06522335473,0.0657459127213,0.0655835646075,0.0657256192071,0.0657915731284,0.0655886379861,0.065532830822,0.0655429775791,0.0654262898723,0.0655962480539,0.065870210496,0.0656419084609,0.0656419084609,0.0654973171721,0.0656013214325,0.0656622019752,0.0655074639292,0.0656393717717,0.0656875688679,0.0658854306317,0.0658879673209,0.065979288135,0.0661238794239,0.0661670031416,0.066179686588,0.0663268145661,0.0662329570628,0.0661365628702,0.0664485756515,0.0661898333451,0.0659716780671,0.0658600637389,0.0656672753537,0.0655987847432,0.0653577992617,0.0654389733186,0.065778889682,0.0659437744851,0.0656469818395,0.0656469818395,0.0658372335354,0.065933627728,0.0662101268593,0.0662963742948,0.066517066262,0.0663826217303,0.0663065210519,0.0662532505771,0.0661670031416,0.0660376319884,0.0660756823276,0.0659995816492,0.0657078623822,0.0656850321787,0.0657864997498,0.0656647386644,0.0654389733186,0.0653654093296,0.0651675475658,0.0652664784477,0.065423753183,0.0654161431151,0.0654389733186,0.0655176106863,0.0653324323689,0.0654618035222,0.065852453671,0.0658930406995,0.0660680722597,0.0662278836843,0.0659970449599,0.065933627728,0.0662152002379,0.0662735440913,0.0662456405092,0.066088365774,0.0659767514457,0.066116269356,0.0660553888133,0.0658423069139,0.0661111959775,0.0659818248243,0.0660325586098,0.0657433760321,0.0655759545397,0.0652461849335,0.0650483231697,0.0649367088415,0.0652385748656,0.0651954511479,0.0650483231697,0.0653451158153,0.0649037318809,0.0651675475658,0.0655861012968,0.0658346968461,0.065979288135,0.0658372335354,0.0659818248243,0.0660503154348,0.0659234809708,0.0658423069139,0.0660427053669,0.0660553888133,0.0658118666426,0.0659742147564,0.0659640679993,0.0662354937521,0.065824550089,0.0656901055572,0.0658828939424,0.066134026181,0.0661822232773,0.0662659340235,0.0663420347018,0.0664460389622,0.0665576532905,0.066362328216,0.0667326848507,0.0668671293825,0.0668772761396,0.066643900726,0.0667605884328,0.0666489741045,0.0666794143759,0.0666641942402,0.0667073179579,0.0666971712008,0.0666185338332,0.0668519092468,0.0664587224086,0.0662735440913,0.0662684707127,0.0662329570628,0.0664079886231,0.0664688691657,0.0663902317981,0.0661188060453,0.0662532505771,0.0662786174698,0.066580483494,0.0668671293825,0.0668595193146,0.0669153264788,0.0667707351899,0.0666591208616,0.0666641942402,0.0670041106035,0.0670599177676,0.0668696660717,0.0670421609427,0.0669812804,0.0670193307392,0.0674505679165,0.0675596455555,0.0676712598838,0.067874195026,0.0681608409145,0.0681177171968,0.0683866062603,0.0684627069387,0.0684753903851,0.0684728536958,0.0683028955141,0.0682699185535,0.068356165989,0.0683789961925,0.0680263963828,0.0679934194221,0.0679122453652,0.067828534619,0.0681075704397,0.068046689897,0.0679528323937,0.0682775286213,0.0684297299781,0.0684677803172,0.0686631053917,0.0689675081051,0.0691476130439,0.0691349295975,0.0692998144006,0.0694063553503,0.0696980746173,0.0695610933963,0.0695027495429,0.069977110438,0.0702180959194,0.0701090182804,0.0701622887553,0.0703221001798,0.0703804440333,0.0706899201252,0.0705224986329,0.0705985993112,0.0705351820792,0.0701749722017,0.0703068800442,0.0704184943724,0.0705427921471,0.0708370481034,0.070578305797,0.0708319747248,0.0710120796636,0.0710983270991,0.071671618876,0.0717883065828,0.071844113747,0.0718009900292,0.0718872374647,0.0719633381431,0.0724376990382,0.072445309106,0.0725696068806,0.0729145966225,0.072600047152,0.0728511793906,0.0728765462833,0.0731809489968,0.0731200684541,0.0733356870428,0.0733864208283,0.0735690624564,0.0736324796883,0.0738252680735,0.0742159182224,0.0740687902443,0.0744518303253,0.0743072390364,0.0745177842466,0.0745101741787,0.0746775956711,0.0746141784391,0.0745862748571,0.0746192518177,0.0745253943144,0.0747942833779,0.0748754574348,0.075222983866,0.075486799551,0.0755248498901,0.0754741161046,0.0755349966473,0.0757252483431,0.0758343259821,0.0763315170807,0.0765217687766,0.0766688967548,0.0770494001465,0.0771863813676,0.0773639496171,0.0775212243524,0.0776429854377,0.0779879751796,0.0783228181644,0.0780234888295,0.0783050613394,0.0781579333613,0.0781604700506,0.0783760886392,0.0782061304576,0.0784800928996,0.0788453761558,0.0790508479873,0.0789798206875,0.0792943701581,0.0791827558298,0.0795201355039,0.0798169281494,0.0800376201167,0.0808189204145,0.0814936797626,0.0821633657321,0.0831146242116,0.0847406420391,0.0863945634487,0.0876705181558,0.0894588840972,0.0907373754936,0.0924978378529,0.093664714921,0.0948163718535,0.096196330821,0.0968939203726,0.0971780295718,0.0974291618104,0.09823836569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m <- 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ycorr <- 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altd  <- c(238)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('Bos_taurus-male-liver-H3K27Ac-ERR572236.50mers.unique.MACS-2.1.0.p1e-1_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) : 238',bty='n')
dev.off()