# R script for Peak Model
#  -- generated by MACS
p <- c(0.0223130061243,0.025971371627,0.0298413781093,0.0331973993556,0.0369162337097,0.0369464681353,0.0361906074943,0.0358277943866,0.0357370911096,0.0362813107712,0.0363720140481,0.0365231861763,0.0367952960071,0.0370674058379,0.0372185779661,0.038246548438,0.0389721746534,0.0393652221867,0.0393349877611,0.0386395959713,0.03857912712,0.0383674861405,0.0385186582688,0.0386395959713,0.0383070172893,0.0372185779661,0.0377930320533,0.0379744386072,0.0374302189456,0.0372185779661,0.03739998452,0.0376720943508,0.0373395156687,0.0372488123918,0.0371278746892,0.0375813910738,0.0364929517507,0.0364324828994,0.036553420602,0.0375209222225,0.0382767828636,0.0389117058021,0.0387907680995,0.0387000648226,0.0393349877611,0.0392745189098,0.0397280352945,0.0394861598893,0.0400001451252,0.039516394315,0.039002409079,0.03857912712,0.0389419402277,0.0393954566124,0.0391233467816,0.0395768631662,0.0398792074227,0.0396978008688,0.0403327238073,0.0411792877253,0.041118818874,0.0412095221509,0.0415723352587,0.0418444450894,0.0423584303254,0.0421467893459,0.0426607745818,0.0431445253921,0.0430840565408,0.0434771040741,0.0439910893101,0.0439608548844,0.0437794483306,0.0435375729254,0.0439003860331,0.0443236679921,0.0439910893101,0.0446260122486,0.0441724958639,0.0437492139049,0.0429631188382,0.043235228669,0.0433561663716,0.0435980417767,0.0439306204588,0.0440213237357,0.0447469499511,0.0446562466742,0.0453214040384,0.0458353892743,0.0467121876179,0.0471959384282,0.0472866417051,0.0477401580898,0.0473168761308,0.0473773449821,0.046621484341,0.0457446859973,0.044928356505,0.0442934335665,0.0443236679921,0.0439608548844,0.0445353089716,0.0444748401204,0.0447771843768,0.0453214040384,0.0460772646794,0.0473471105564,0.0478308613667,0.0471657040026,0.0465005466384,0.0463796089358,0.0462586712333,0.0459865614025,0.0461377335307,0.0464703122128,0.0468633597461,0.0468935941718,0.0474075794077,0.0485564875821,0.0496146924796,0.0497356301822,0.0489495351155,0.0494030515001,0.0489495351155,0.0485867220078,0.0481332056231,0.0488285974129,0.0485262531565,0.0484355498795,0.0480122679205,0.0486169564334,0.0494635203514,0.049917036736,0.0502193809925,0.0500379744386,0.050763600654,0.0500682088642,0.050854303931,0.05127758589,0.0519125088285,0.0517311022746,0.052033446531,0.0519125088285,0.05245672849,0.0526381350439,0.0522450875105,0.0517311022746,0.0520939153823,0.0518822744028,0.0520032121054,0.0527590727464,0.0526079006182,0.0530614170029,0.0530009481516,0.0535451678132,0.0541800907517,0.0549661858184,0.0543010284542,0.0551778267979,0.0555406399056,0.0552382956491,0.0557522808851,0.0555104054799,0.056266266121,0.0566593136544,0.056266266121,0.0566593136544,0.0572942365928,0.0570221267621,0.0572337677416,0.0580803316596,0.0578989251057,0.0582315037878,0.0573244710185,0.0576570497006,0.0582315037878,0.0576268152749,0.057536111998,0.0579291595313,0.0578082218288,0.0571732988903,0.0575058775723,0.0573244710185,0.0581408005108,0.0582315037878,0.0577779874031,0.0577477529775,0.0583222070647,0.0588966611519,0.0594711152391,0.0597129906443,0.0605293201366,0.0615270561828,0.0622224479726,0.0617386971623,0.06210151027,0.0628573709111,0.0628876053367,0.0620712758444,0.0615572906085,0.061678228311,0.0610735397982,0.0616479938854,0.0613758840546,0.0614061184802,0.06210151027,0.0633108872957,0.0634015905727,0.0645202643214,0.0656691724959,0.06633432986,0.0671204249267,0.0669692527985,0.0669087839472,0.0679065199934,0.0675134724601,0.0666064396908,0.0667273773934,0.0670599560754,0.0675437068857,0.0674227691831,0.0678460511421,0.0684809740806,0.0689647248909,0.0692066002961,0.0705369150243,0.0702950396192,0.0710206658346,0.0702043363423,0.0702345707679,0.0710509002603,0.069720585532,0.0693880068499,0.070143867491,0.0705973838756,0.0706276183013,0.071413713368,0.0711113691115,0.0722905117116,0.0728347313732,0.0725626215424,0.0740138739732,0.0744976247835,0.0751930165733,0.0752232509989,0.0745883280604,0.0762512214708,0.0761605181939,0.0756767673836,0.0749209067425,0.0753744231272,0.0754651264041,0.0751627821477,0.0742557493784,0.0744371559322,0.0745278592092,0.0734696543117,0.0741650461015,0.0752534854246,0.0761000493426,0.0757674706605,0.0755255952554,0.0759488772144,0.0761000493426,0.0761000493426,0.0771582542401,0.0778536460299,0.0775210673478,0.0770675509631,0.0765233313016,0.0773396607939,0.0789118509274,0.0790932574812,0.0788513820761,0.0799095869736,0.0792444296094,0.0790025542043,0.0806049787633,0.0816329492352,0.0821167000455,0.0819957623429,0.0817236525121,0.0826004508558,0.0834772491994,0.0828423262609,0.0836888901789,0.08444475082,0.0846866262251,0.0855634245687,0.0861983475072,0.0864099884867,0.0868635048714,0.0858355343995,0.0868030360201,0.0877705376407,0.0878310064919,0.0893124933484,0.0896753064561,0.0893729621997,0.0920033572306,0.0965989899283,0.0996829013439,0.10421806519,0.107604320862,0.112048781432,0.11740027477,0.121874969766,0.126591540166,0.130249905669,0.13218490891,0.132608190869,0.133243113807,0.135782805561,0.137748043228,0.138231794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m <- 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ycorr <- 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altd  <- c(275)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('BCL6_UV-ChIP-seq_merged-vs-minusUV_control_ChIP-GSM2754206.dedup.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) : 275',bty='n')
dev.off()