# R script for Peak Model
#  -- generated by MACS
p <- c(0.0382379199522,0.0450252143746,0.0514307234857,0.0583452796785,0.0645217176029,0.064555654075,0.0642078052359,0.0644538446587,0.064547169957,0.0647338205536,0.0647932093798,0.0639702499311,0.0643520352423,0.0634612028494,0.0639787340491,0.064547169957,0.0652852882254,0.0647762411437,0.0644199081866,0.064538685839,0.064852598206,0.0652343835173,0.0649374393863,0.0651749946911,0.0649798599764,0.0643690034784,0.0634357504953,0.0636902740362,0.0641314481736,0.0646150429012,0.0647762411437,0.0649459235043,0.064250225826,0.0644199081866,0.0643944558325,0.0641314481736,0.0645726223111,0.0648356299699,0.0650986376288,0.06423325759,0.0640975117015,0.0639617658131,0.0647932093798,0.0651919629271,0.0653955817598,0.065141058219,0.0653192246975,0.0649713758584,0.064250225826,0.0648101776159,0.0651156058649,0.0648695664421,0.0646150429012,0.0641484164097,0.0636733058001,0.0640550911114,0.0636902740362,0.0637326946263,0.0636648216821,0.0630963857742,0.0626721798728,0.0631727428365,0.0633169728429,0.0639617658131,0.0645811064291,0.0646744317274,0.0645726223111,0.0649968282125,0.0649798599764,0.0654125499958,0.0649544076223,0.0649798599764,0.0644962652488,0.063953281695,0.0639193452229,0.0635630122657,0.0638599563967,0.0634272663773,0.0636902740362,0.0636817899181,0.0638260199246,0.063647853446,0.0638599563967,0.0634357504953,0.0627909575252,0.0636054328559,0.0631897110725,0.0639872181671,0.0643011305342,0.0636987581542,0.0642756781801,0.0641144799376,0.0641314481736,0.0647253364356,0.0652598358713,0.0647592729077,0.0653786135237,0.0647677570257,0.0645047493669,0.0649628917404,0.064555654075,0.0647168523176,0.064844114088,0.0646320111373,0.0644199081866,0.0645302017209,0.0645217176029,0.0646913999635,0.0649204711502,0.0650562170387,0.0649289552683,0.0649968282125,0.0649119870322,0.0649035029142,0.0647338205536,0.0644708128947,0.0640635752294,0.0643435511243,0.0640296387573,0.0639787340491,0.0645811064291,0.0644453605407,0.0644199081866,0.0636648216821,0.0636817899181,0.0645217176029,0.064547169957,0.0644538446587,0.0646659476094,0.0643435511243,0.0638938928688,0.0637920834525,0.0641569005277,0.0650647011567,0.065768882953,0.0649204711502,0.0652174152812,0.0646404952553,0.0650392488026,0.0656161688285,0.0657773670711,0.0663288347429,0.0664815488674,0.0667869771164,0.0669566594769,0.0667784929984,0.0666088106378,0.067262087726,0.0671517941916,0.0670245324212,0.0671348259555,0.0670415006572,0.0671687624276,0.0671433100736,0.0664900329854,0.0673045083161,0.0679238489321,0.0677371983355,0.0674063177324,0.0675250953848,0.067567515975,0.06788991246,0.0675420636209,0.0673299606702,0.0673129924341,0.0673045083161,0.0668887865327,0.0672536036079,0.0674996430307,0.0678135553978,0.0681189836468,0.0674996430307,0.0676608412733,0.0679323330502,0.0682038248271,0.0677711348076,0.0680086901124,0.0671942147817,0.06728754008,0.0668209135885,0.066379739451,0.0668463659426,0.0671008894834,0.0671772465457,0.0676523571552,0.0679153648141,0.0679662695223,0.0689504272135,0.0691625301642,0.0694170537051,0.0701042672653,0.0700618466752,0.0701466878555,0.0703927272783,0.0701042672653,0.0703418225701,0.070613314347,0.0710375202484,0.0711902343729,0.0712750755532,0.0710969090746,0.0716907973366,0.0718859320512,0.0717247338087,0.0720640985298,0.0726919232639,0.072725859736,0.0720556144118,0.0722337808904,0.0729040262146,0.0733621685881,0.072742827972,0.073022803867,0.0731924862275,0.0735573033027,0.0734554938864,0.0738203109616,0.0742699692171,0.0738881839058,0.0737863744895,0.0740748345024,0.0747111433545,0.0743887468695,0.0744990404038,0.0741596756827,0.0744396515776,0.0737863744895,0.0736082080109,0.0744566198137,0.0744057151055,0.0739815092041,0.0739815092041,0.0741681598007,0.0740578662664,0.0743293580433,0.0746178180562,0.075143833374,0.0757886263441,0.0756528804556,0.0752710951444,0.0762722210717,0.0767303634452,0.0767812681534,0.077281831117,0.0770357916942,0.0767049110911,0.0767812681534,0.076679458737,0.076679458737,0.0774090928874,0.0767812681534,0.0771206328745,0.0780454017395,0.0782999252804,0.0790041070767,0.0792501464995,0.0796573841649,0.0804124706693,0.0800731059482,0.079699804755,0.0799034235877,0.079699804755,0.0790380435488,0.079411344742,0.0793604400339,0.0799373600598,0.0804464071415,0.0801579471285,0.0807348671544,0.0809893906952,0.0808960653969,0.0806415418561,0.0809639383412,0.0806415418561,0.081209977764,0.0811251365837,0.0815747948392,0.0816850883735,0.0820753578028,0.0829661901958,0.0839248955329,0.0844169743786,0.0848072438078,0.084552720267,0.0846714979194,0.0846969502735,0.0841539667197,0.0839842843591,0.0842642602541,0.0837382449363,0.0836109831659,0.0840182208312,0.0841454826017,0.0853332591256,0.0852569020633,0.0850617673487,0.0850617673487,0.0860883456301,0.086079861512,0.086979178023,0.087267638036,0.0878021374717,0.0882857321993,0.0890662710579,0.0904237299424,0.0920781329578,0.0938937342158,0.0949118283792,0.0962862554997,0.096964984942,0.0977285555645,0.0980848885217,0.0987721020819,0.099094498567,0.099408410934,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m <- 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ycorr <- 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altd  <- c(257)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('Oryctolagus_cuniculus-male-liver-H3K4me3-ERR572153.50mers.unique.MACS2_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) : 257',bty='n')
dev.off()