# R script for Peak Model
#  -- generated by MACS
p <- c(0.0248356807012,0.029172069395,0.0334871490535,0.0374293205934,0.0417124366988,0.0418935634993,0.0423090896887,0.0425008710068,0.0427139613603,0.0430442514083,0.0437581040925,0.0443227935293,0.0442908299763,0.0443867206354,0.0443654116,0.0448768284484,0.0446850471303,0.0450686097666,0.0451112278373,0.0447489742363,0.0446424290596,0.0442482119056,0.0444506477414,0.0445678474358,0.0444506477414,0.0440670851051,0.0440670851051,0.043576977292,0.0434704321153,0.0438646492693,0.0440244670344,0.0442588664232,0.0442695209409,0.0443654116,0.0449194465191,0.0449833736252,0.045185809461,0.0454415178852,0.0459316256983,0.0455054449913,0.0449301010368,0.0450153371782,0.0452497365671,0.0453882452968,0.0452284275317,0.045153845908,0.0449087920014,0.0452284275317,0.045185809461,0.0458037714862,0.046432388029,0.0464536970644,0.0460914434634,0.0465282786881,0.0467200600062,0.0468052961476,0.0470929681249,0.0473912946198,0.0477428937031,0.0475937304556,0.0470290410188,0.0465282786881,0.0472740949254,0.0470929681249,0.0471249316779,0.0470503500542,0.046858568736,0.0468052961476,0.0469438048774,0.0471462407133,0.0475617669026,0.0478281298445,0.0481477653747,0.0481584198924,0.0484034737989,0.0487124548115,0.0493410713544,0.0486485277055,0.0478281298445,0.0477961662915,0.0479666385743,0.0479986021273,0.0477322391854,0.048105147304,0.0477961662915,0.0480838382687,0.0480518747157,0.0487657273999,0.0494263074958,0.0495008891195,0.04968201592,0.050076233074,0.0502253963214,0.0498737972381,0.0502253963214,0.0503639050512,0.0502999779451,0.0498737972381,0.0499057607912,0.0500442695209,0.050470450228,0.0500336150033,0.0501295056623,0.0504278321573,0.0501295056623,0.0502893234275,0.0506089589577,0.051290848089,0.051717028796,0.0515572110308,0.0517383378313,0.05211124595,0.0521964820914,0.0521645185383,0.0532725883766,0.0533152064473,0.0534430606594,0.0531980067528,0.0527611715281,0.0531340796468,0.0529849163993,0.0533791335533,0.0530168799524,0.0534963332477,0.0532512793412,0.0531873522352,0.0531980067528,0.0536987690836,0.0542634585204,0.0545298214622,0.0545937485683,0.0549346931339,0.0552117105935,0.0553928373939,0.0549773112046,0.0555633096768,0.0558083635833,0.0557018184065,0.0559788358661,0.0565222162675,0.0566500704796,0.0567992337271,0.0570442876336,0.0570762511866,0.0579392671183,0.057917958083,0.0579925397067,0.0585465746258,0.0577794493532,0.0577048677295,0.0584719930021,0.0585891926965,0.0586957378733,0.0586957378733,0.0585465746258,0.0584293749314,0.0584613384844,0.0582162845779,0.059196500204,0.0592497727924,0.0588342466031,0.0594308995929,0.0594095905575,0.0597718441585,0.0598464257822,0.0608586049614,0.0608586049614,0.0613700218098,0.0613913308451,0.0622010741885,0.0624994006834,0.0621051835294,0.0627124910369,0.0633624166151,0.0640123421933,0.0637885973221,0.0639271060519,0.0644278683826,0.0648966671603,0.0645876861477,0.0654187385264,0.066153900246,0.0664841902939,0.0664628812586,0.0664948448116,0.0670595342484,0.0679651682508,0.0677201143443,0.0676348782029,0.0680077863215,0.0676774962736,0.0672726246019,0.0674644059201,0.0674963694731,0.0679332046978,0.0678692775917,0.0681782586043,0.068615093829,0.0688601477355,0.0683487308871,0.0683487308871,0.069073238089,0.069467455243,0.0698829814324,0.0693609100663,0.0695420368668,0.0699469085384,0.0700214901622,0.0706074886343,0.0712787232478,0.0716622858841,0.0721523936972,0.0720458485205,0.0724187566391,0.0730899912526,0.0742406791616,0.0740169342904,0.0742193701262,0.0748479866691,0.0753380944821,0.0751569676817,0.0747627505277,0.0754766032119,0.0758601658482,0.0761904558962,0.0753594035175,0.0754766032119,0.0758601658482,0.0757749297068,0.0760839107194,0.0769043085804,0.0780869600424,0.0782148142545,0.0784385591256,0.0791417572922,0.0796957922113,0.080132627436,0.0802924452012,0.0808145165672,0.0816349144282,0.0827536387841,0.0827749478195,0.0830519652791,0.0837125453749,0.0838723631401,0.0842772348117,0.0841919986703,0.0849058513546,0.0852574504378,0.0848419242485,0.084170689635,0.0845222887183,0.0855451224151,0.0853320320616,0.085481195309,0.0861630844402,0.0872924633138,0.087484244632,0.0875375172204,0.0881341702102,0.0888267138591,0.0891676584247,0.0887947503061,0.0899667472503,0.0904142369927,0.0901798376038,0.0905953637932,0.0907871451113,0.0909682719118,0.091586233937,0.0921402688561,0.0927901944343,0.0930778664115,0.0926410311868,0.0933335748357,0.0935999377776,0.0937384465074,0.0943990266033,0.0948465163456,0.0946866985805,0.0952726970526,0.0950169886284,0.096082440396,0.0970093834337,0.0965512391737,0.0974675276938,0.0980854897189,0.0983944707315,0.0984690523552,0.0989804692036,0.0992468321455,0.0993533773223,0.0999713393475,0.0996623583349,0.10059995589,0.101132681774,0.101004827562,0.101292499539,0.102357951307,0.103157040132,0.103988092511,0.10545841595,0.106321431882,0.108100736334,0.108995715818,0.109698913985,0.110988110624,0.112181416603,0.112852651217,0.11398203009,0.11425904755,0.114610646633,0.114227083997,0.113971375573,0.114642610186,0.115484317083,0.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m <- 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ycorr <- 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altd  <- c(241)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('Callithrix_jacchus-male-liver-H3K4me3-ERR572225.50mers.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) : 241',bty='n')
dev.off()