# R script for Peak Model
#  -- generated by MACS
p <- c(0.0573574285043,0.0661572851728,0.0752428111474,0.0844649615728,0.0935070161313,0.0924016001207,0.0911844004686,0.0910167250063,0.0912278718848,0.0919234145431,0.0913086045148,0.09226497567,0.0925568551784,0.0912154514802,0.09186131252,0.0929170469122,0.0938920486743,0.0933890222875,0.0933455508713,0.0926748490222,0.09226497567,0.0914514391678,0.0917060574624,0.0922090838492,0.0912092412778,0.0900479334465,0.0896753213081,0.0891722949213,0.089004619459,0.0887500011644,0.088700319546,0.0897250029266,0.0899982518281,0.089774684545,0.0889549378405,0.0889611480428,0.0889735684475,0.0893151295743,0.0890791418867,0.0887189501529,0.0890232500659,0.0880109870899,0.0880855095176,0.0897187927243,0.0903770741688,0.0892033459328,0.0892840785628,0.0888369439967,0.0883401278122,0.0878805728415,0.0869676731024,0.0864956977271,0.0850984022081,0.0841606616598,0.0841979228736,0.0849679879597,0.0855641673811,0.085197765445,0.086452226311,0.086452226311,0.0876197443446,0.0883711788237,0.087303024027,0.0878184708184,0.0875079607031,0.0886257971183,0.0874272280731,0.0878060504138,0.087141558767,0.0876756361654,0.0880109870899,0.0875452219169,0.0877936300092,0.087141558767,0.087222291397,0.0865453793456,0.0863777038833,0.0860734039702,0.0858684672941,0.0857070020342,0.0847816818905,0.084508432989,0.0853219694911,0.0864025446925,0.0871974505877,0.0886257971183,0.0881476115407,0.0884394910491,0.0887313705575,0.0889797786498,0.0902963415388,0.0899423600073,0.091252712694,0.0910477760179,0.0905695904403,0.088681688939,0.0893834417997,0.0894455438228,0.0887500011644,0.088458121656,0.08744585868,0.0872098709924,0.0863901242879,0.0852163960519,0.0855641673811,0.0860423529587,0.0858312060803,0.0856200592019,0.086899360877,0.0875017505008,0.0867813670332,0.0884519114537,0.0889735684475,0.0901472966834,0.089631849892,0.0900603538511,0.0905882210472,0.0899547804119,0.089166084719,0.0889984092567,0.0898367865681,0.0891412439097,0.0890170398636,0.0878371014253,0.0880979299222,0.0881662421476,0.0887251603552,0.089631849892,0.0902466599203,0.0896380600943,0.0899113089958,0.0896815315104,0.0893648111928,0.0896380600943,0.089693951915,0.0899609906142,0.0889052562221,0.0880979299222,0.0873402852408,0.0882904461937,0.0888183133898,0.0889859888521,0.0880482483038,0.0878433116276,0.0873899668593,0.0873278648362,0.0873775464546,0.0879550952692,0.0882407645753,0.0886009563091,0.0869242016863,0.0864770671202,0.0878371014253,0.0878060504138,0.0889797786498,0.0883711788237,0.0886444277252,0.087911623853,0.0879364646622,0.0876507953561,0.0886568481298,0.0884457012514,0.0870980873508,0.08760732394,0.0870421955301,0.0865391691432,0.0860671937679,0.0865081181317,0.0862472896348,0.0848065226997,0.0846450574397,0.0848065226997,0.0849679879597,0.084042667816,0.0827385253316,0.0816827909394,0.081713841951,0.0824528560255,0.0818504664017,0.0823286519793,0.0816020583095,0.0815585868933,0.0819995112571,0.0831608190884,0.0841606616598,0.0854461735373,0.084974198162,0.084104769839,0.083719737296,0.0835831128453,0.083092506863,0.0817448929625,0.0813660706218,0.0797389976175,0.0788012570692,0.0778697267232,0.0773977513478,0.0775095349894,0.0772300758856,0.0760377170427,0.0755036396443,0.0764600107995,0.0753173335751,0.0756775253089,0.0753049131705,0.0760190864358,0.0756961559158,0.0748018867837,0.0752241805405,0.0751620785175,0.075416696812,0.0747025235468,0.0748453581998,0.0746155807145,0.0743609624199,0.0733673300508,0.0730630301378,0.0729574566986,0.0723053854564,0.0728953546755,0.0731934443862,0.0743485420153,0.0742057073622,0.07371510138,0.0742057073622,0.0745907399052,0.0749074602229,0.0742740195876,0.0742802297899,0.07347290349,0.0725848445602,0.0714918489542,0.0712807020758,0.0715663713819,0.0707652552843,0.0705106369898,0.070150445256,0.070069712626,0.069765412713,0.0711937592435,0.0723923282887,0.0720631875664,0.0720445569595,0.0720631875664,0.0718893019018,0.0720010855434,0.0722432834333,0.0734853238947,0.0738951972469,0.0737399421892,0.0736095279408,0.0739138278538,0.0751496581128,0.0748205173906,0.0746776827375,0.0753173335751,0.0755036396443,0.074950931639,0.0749881928529,0.0742926501945,0.0733859606577,0.0734604830854,0.0727152588086,0.0726096853694,0.0742926501945,0.0735474259177,0.0741187645299,0.0745037970729,0.0743237012061,0.0752117601359,0.0750875560898,0.075031664269,0.0743858032291,0.0736157381431,0.0722805446472,0.0724171690979,0.072317805861,0.0723240160633,0.0725724241556,0.071690575428,0.0721252895895,0.0727587302248,0.0735412157154,0.0745783195006,0.0751496581128,0.0751496581128,0.0751310275059,0.0752800723613,0.0754291172166,0.0764351699903,0.0770934514348,0.0767456801056,0.0770189290071,0.0771928146717,0.0778138349024,0.0776523696424,0.07804982259,0.0777393124747,0.078068453197,0.0776710002493,0.07821128785,0.078596320393,0.0784100143238,0.0788012570692,0.0791800794099,0.079993615912,0.0804407504781,0.0815461664887,0.0827509457362,0.0836700556776,0.0830117742331,0.0841606616598,0.0848003124974,0.0852909184796,0.0858684672941,0.08677515683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m <- 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ycorr <- 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xcorr <- 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altd  <- c(172, 354, 565)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('LUC-H3K4me3_snap-chip_control-vs-LUC-IgG.2x25mers.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) : 172,354,565',bty='n')
dev.off()