# R script for Peak Model
#  -- generated by MACS
p <- c(0.0394874947582,0.0462008974815,0.0529696788549,0.059783770033,0.0663209679604,0.0665072416018,0.0664241736266,0.0664317252607,0.066406553147,0.0664468285289,0.0663486572855,0.0661422459531,0.0658653527025,0.0655884594518,0.0658779387593,0.066434242472,0.0666054128452,0.0665198276586,0.0666054128452,0.0663763466105,0.0669099954209,0.0670559936804,0.067353024622,0.0675669875885,0.0675594359544,0.0672170952081,0.0671667509807,0.0673933000039,0.0671440960783,0.0671189239646,0.0667388250478,0.0666557570726,0.0666356193816,0.0667161701455,0.0665928267883,0.0669074782096,0.0669704084938,0.0670031322416,0.0672246468422,0.0673630934675,0.0673681278902,0.0674788851905,0.0672875771264,0.0672598878013,0.0673303697197,0.0670912346396,0.0669704084938,0.067101303485,0.0671969575171,0.0669477535915,0.0668772716731,0.0669301331119,0.0668747544618,0.0669452363801,0.0670333387781,0.0671566821352,0.0675191605724,0.0673857483698,0.0673303697197,0.0674788851905,0.067856466896,0.0675795736453,0.0676399867182,0.0676122973931,0.0676878137342,0.0673857483698,0.0674033688494,0.0672045091512,0.0674310581745,0.0674637819223,0.0675695047998,0.0678212259368,0.0680578438056,0.0683422886904,0.0683473231131,0.0685612860795,0.0685512172341,0.069102486524,0.0692082094016,0.0693516904497,0.0688608342325,0.068891040769,0.0689841775897,0.0686795950139,0.0685386311772,0.0687173531845,0.0686040786728,0.0683850812836,0.0681232913012,0.0681736355286,0.0685587688682,0.0685411483886,0.0688155244279,0.0687022499162,0.0686468712661,0.0687173531845,0.0690848660445,0.0689967636465,0.0693315527587,0.0691855544992,0.0691628995969,0.0692761741086,0.0691125553695,0.0695631362047,0.0699407179102,0.0699558211784,0.0695757222616,0.0700011309831,0.0697393410006,0.0701144054947,0.0701018194379,0.0700993022265,0.0700439235764,0.0700464407877,0.0698047884962,0.0697544442688,0.0703585749976,0.0702755070224,0.0704970216229,0.0705171593139,0.0708519484261,0.0709324991899,0.0708947410194,0.0704265397046,0.0707286050689,0.0709778089946,0.071028153222,0.0706077789232,0.0706279166142,0.0704693322979,0.0702780242337,0.0702780242337,0.0707839837191,0.071375528391,0.0712320473429,0.0713679767569,0.0712244957088,0.0715366299187,0.0715894913574,0.0718613501854,0.0720551754608,0.0724856186051,0.0722917933296,0.0723748613048,0.072525893987,0.0720853819973,0.0720350377699,0.0724906530278,0.0724881358164,0.0729034756925,0.0730469567405,0.0729664059767,0.0730796804883,0.0728908896356,0.0731300247157,0.0737064661194,0.0737593275582,0.073812188997,0.0739607044678,0.0738348438993,0.0736385014124,0.0737492587127,0.0738096717856,0.0740613929226,0.0739204290859,0.0739103602404,0.0737794652492,0.0738272922652,0.0739808421587,0.0738726020698,0.0740739789794,0.074343320596,0.0743735271324,0.0743810787665,0.0744893188554,0.0741721502228,0.0745044221237,0.0745346286601,0.0746881785537,0.0748769694064,0.0749323480565,0.0750884151615,0.0750179332431,0.0750481397795,0.0752797232256,0.0756875114675,0.0755717197445,0.0755968918582,0.0755540992649,0.0756522705083,0.0759870596205,0.075725269638,0.0761934709528,0.0764527437239,0.0765358116991,0.0766314657312,0.0767346713973,0.0768202565839,0.0770568744526,0.0770845637777,0.0770468056072,0.0771978382894,0.0771625973302,0.0770140818594,0.0772280448258,0.0772758718418,0.0777415559452,0.0779227951639,0.0779832082367,0.0783104457148,0.0782047228373,0.0783280661944,0.078509305413,0.0785420291608,0.078481616088,0.0787585093386,0.0785546152177,0.078781164241,0.0788667494275,0.0787509577045,0.0790328853779,0.0793450195878,0.0792745376695,0.0797024636023,0.0797628766752,0.0798610479186,0.0799768396416,0.0801857681853,0.0804299376882,0.0806287973864,0.0806791416138,0.0807546579549,0.0810567233193,0.0811825838878,0.0816860261617,0.0818622309576,0.0820610906558,0.082048504599,0.082116469306,0.0822851224677,0.0825368436047,0.082599773889,0.0830604235696,0.0832114562518,0.0829723211717,0.0829748383831,0.0830855956833,0.0831409743335,0.0830679752038,0.083110767797,0.0833272479748,0.0834732462343,0.0833398340317,0.0832819381702,0.0836016240142,0.0837904148669,0.0837425878509,0.0839641024514,0.0843265808887,0.0846588527895,0.0847469551874,0.084812402683,0.0848098854717,0.0851346057384,0.0850565721859,0.0852579490955,0.0856783233943,0.0857764946377,0.0859451477995,0.0858645970356,0.0857488053126,0.0858822175152,0.0858243216537,0.085731184833,0.0859073896289,0.0859073896289,0.0862497303752,0.0863277639277,0.0865215892031,0.0868009996652,0.0872364772322,0.0876442654741,0.0878783661315,0.0880243643909,0.0884699108034,0.088515220608,0.0887921138587,0.0888449752975,0.0888676301998,0.0888701474112,0.0887216319404,0.0887619073223,0.0888198031838,0.0892401774825,0.0892854872872,0.0895472772696,0.0892880044986,0.0896957927405,0.0898090672521,0.0905415757607,0.0908260206455,0.0912187056192,0.0921979008421,0.0931066141466,0.0937132620867,0.094634561448,0.0956238255164,0.0962657144157,0.0969302582173,0.097207151468,0.098289552357,0.0986897889648,0.0989792682723,0.0990170264429,0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m <- 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ycorr <- 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altd  <- c(295)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('Monodelphis_domestica-male-liver-H3K4me3-ERR572252.50mers.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) : 295',bty='n')
dev.off()