# R script for Peak Model
#  -- generated by MACS
p <- c(0.0425674680037,0.0496877748442,0.0569092020087,0.0639349703214,0.0710869894528,0.0712180270325,0.0715303631813,0.0715136095181,0.0715644688527,0.0715525019505,0.0715459201542,0.0715034376512,0.0713293192235,0.0715369449775,0.0716213116384,0.0715525019505,0.0712664929866,0.0713712033813,0.0713029920385,0.0713538513731,0.0713520563377,0.0714071040881,0.071401120637,0.0713484662671,0.0712449525626,0.0712802549242,0.0713364993648,0.0713424828159,0.0713347043295,0.0713137622505,0.071321540737,0.0713167539761,0.0713897520798,0.0712838449949,0.071321540737,0.0713077787994,0.0712868367205,0.071236575731,0.0712904267911,0.0712778615438,0.0713783835227,0.0713945388407,0.071231190625,0.0712802549242,0.0711450289288,0.071114513328,0.0711528074152,0.0711581925212,0.0710917762137,0.0710857927626,0.0708638067258,0.0707495228093,0.0708853471499,0.0708255126386,0.0708691918318,0.0708799620439,0.0709086826093,0.0709487717318,0.07093919821,0.0708548315491,0.0709026991581,0.0710223681807,0.0709481733867,0.0710068112077,0.0709104776446,0.0708871421852,0.07083269278,0.0708895355657,0.0709104776446,0.0710379251536,0.0710498920558,0.0710911778686,0.0712150353069,0.0711707577686,0.0711791346002,0.0712090518558,0.0713233357723,0.0712228137934,0.0712910251362,0.071337696055,0.0713023936934,0.071199478334,0.071258116155,0.0712515343588,0.0713771868325,0.0712437558723,0.0711085298769,0.0711444305836,0.0709840740935,0.0709403949002,0.0709206495115,0.0709792873326,0.0709140677153,0.0708644050709,0.0708530365138,0.0709733038814,0.0710977596649,0.0711133166378,0.0711605859017,0.0710881861431,0.071135455407,0.0710457036401,0.0710486953656,0.0711480206543,0.0711952899182,0.0712096502009,0.0710702357897,0.0709134693702,0.0710642523386,0.0711635776273,0.0711097265671,0.0712766648535,0.0712593128453,0.0711922981927,0.0710977596649,0.0710845960724,0.0710463019852,0.0711851180513,0.0711522090701,0.0710822026919,0.0712270022092,0.0711958882633,0.0711330620265,0.0711731511491,0.0712587145002,0.0713305159137,0.0715267731106,0.0714669385994,0.0715046343415,0.0715166012437,0.07152318304,0.0714878806783,0.0715878043121,0.0716865312557,0.0716284917798,0.0714944624745,0.0715249780753,0.0716398603369,0.071624303364,0.0717756846775,0.0716751626986,0.0717236286527,0.0716943097422,0.0716673842121,0.0717750863324,0.0719659584233,0.0718827884527,0.0718391092594,0.0717822664737,0.0717708979166,0.0719498031053,0.0719450163444,0.0720126293421,0.0720581035707,0.0720156210677,0.0719498031053,0.0719761302902,0.0720826357203,0.0722824829879,0.0722764995368,0.0722268368924,0.072378816551,0.0723794148961,0.0724739534239,0.0725840489247,0.0727174798848,0.0728018465457,0.0727743226705,0.0727168815397,0.0728317638013,0.0728084283419,0.0727809044667,0.0730058822291,0.0728598860216,0.0727623557682,0.0726319165337,0.0725936224465,0.0727533805915,0.0727354302382,0.0726091794194,0.0727288484419,0.0727138898141,0.0726486701968,0.0729424576471,0.0731369198088,0.0732188930892,0.0732906945027,0.0732978746441,0.0733289885899,0.0734588294794,0.0735378110342,0.0736508982605,0.0736568817116,0.0736305545267,0.0737687722477,0.0738615157402,0.0739913566296,0.0740978620597,0.0743078811942,0.0744490906408,0.074546022549,0.0744987532851,0.0745807265656,0.0746638965362,0.0746435528024,0.0748368182738,0.0748302364775,0.0747572383738,0.0748200646106,0.0748781040865,0.0749684541986,0.0751688998113,0.0752215541812,0.0752795936571,0.0753537884511,0.0753190844346,0.0753801156361,0.0755368820556,0.0756427891405,0.0756990335811,0.0757086071029,0.0758863156014,0.0760897529397,0.0761352271682,0.0762890018622,0.076426022893,0.0765169713501,0.0765809942771,0.076553470402,0.0766318536117,0.0767868249959,0.0767946034823,0.0768783717981,0.0770824074815,0.0772074616101,0.0773097786243,0.0775491166694,0.0776735724528,0.0777298168934,0.0779141071881,0.0779673599031,0.0780445464227,0.0781097660399,0.0781785757279,0.0781749856572,0.0782473854158,0.0782737126008,0.0783221785549,0.0785387794857,0.078550746388,0.0787428151691,0.0788882130315,0.0790096770894,0.0791556732968,0.0791915740036,0.0792992761239,0.0793579139449,0.0795828917073,0.0796660616779,0.0798210330621,0.0800131018433,0.080144737768,0.0802955207364,0.0803870675387,0.0804947696589,0.0806778632634,0.0809070294416,0.0810727710378,0.0811714979813,0.0813940823632,0.0813623700723,0.0814760556437,0.081663936009,0.0817130003083,0.0820295248729,0.0821114981533,0.0822096267518,0.0823035669345,0.0824794803976,0.0824878572292,0.0827361704509,0.0828390858103,0.0829982456102,0.0832986148568,0.0834487994801,0.0836636053755,0.0838407155288,0.0839699580732,0.0842475902054,0.0845222306122,0.0846030072024,0.0848208048234,0.0849314986692,0.084983554694,0.085132542627,0.0853587170796,0.0856943886878,0.0859121863088,0.0862017853433,0.08655600565,0.086959290256,0.0874349746205,0.0878526195091,0.0884766934616,0.0891306846697,0.0896674002358,0.090220869465,0.0910334221279,0.0915246634654,0.0919662421586,0.0924167960284,0.0928254657403,0.0932694378139,0.0935428815304,0.09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m <- 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ycorr <- 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altd  <- c(258)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('A549-100nM-Dex-2h-H3K27ac.pooled.sorted.pseudoRep2.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) : 258',bty='n')
dev.off()