# R script for Peak Model
#  -- generated by MACS
p <- c(0.0398050943266,0.0463446211231,0.052996076429,0.0593905107134,0.0658118907501,0.0660440387695,0.0660005110158,0.0658906552566,0.0660751300221,0.065907237258,0.0658139635002,0.0659507650117,0.0659238192594,0.0663362965439,0.0665352805605,0.066541498811,0.0664565160539,0.0664834618062,0.0662119315335,0.0663632422961,0.0663549512954,0.0663508057951,0.066433715802,0.066110366775,0.0658989462573,0.0657890904982,0.065894800757,0.0659880745148,0.0657434899943,0.0658616367542,0.0657165442421,0.0656854529895,0.0654781779722,0.0655735244801,0.0657103259916,0.0657310534933,0.0657559264954,0.0653973407154,0.0655051237244,0.0652709029549,0.0653393037106,0.0652646847043,0.0652854122061,0.0653703949632,0.065308212458,0.0653475947113,0.0651672654462,0.0652294479514,0.0653621039625,0.0652418844524,0.0652667574545,0.0653351582102,0.0653828314642,0.0654242864677,0.0653538129618,0.0651569016953,0.0653165034587,0.0652833394559,0.0650967919403,0.0652522482033,0.0651195921922,0.0650346094351,0.0649309719264,0.0649392629271,0.0650180274337,0.0649848634309,0.0647299151596,0.0647547881617,0.0647216241589,0.0645744588966,0.0645454403942,0.0645951863984,0.0645392221437,0.0642842738724,0.0642283096177,0.0644065661326,0.0643568201285,0.0643319471264,0.0643962023818,0.064410711633,0.0643858386309,0.0642303823679,0.0642863466226,0.064147472361,0.063909106091,0.0638759420883,0.0640085980994,0.0640085980994,0.0641163811084,0.0639878705976,0.0639339790931,0.0640624896039,0.064112235608,0.0643692566295,0.0647008966572,0.0645848226475,0.0645620223956,0.0646718781548,0.0644894761395,0.0647382061603,0.0649309719264,0.0648148979167,0.0645288583928,0.0642759828717,0.0640935808565,0.0643215833755,0.0642324551181,0.0641972183651,0.0641495451111,0.0641101628578,0.0641681998627,0.0642573281201,0.0643174378752,0.064435584635,0.0644583848869,0.064172345363,0.0644666758876,0.0645164218918,0.064638714152,0.0646034773991,0.0644604576371,0.0643132923748,0.0642759828717,0.0644563121368,0.0644666758876,0.0646490779029,0.0645060581409,0.0644210753838,0.0644521666364,0.0646159139001,0.064673950905,0.0648169706669,0.0652025021991,0.0649143899251,0.065105082941,0.0651258104427,0.0651341014434,0.0651486106946,0.0651361741936,0.065152756195,0.0651610471957,0.0651195921922,0.0648708621714,0.0651465379445,0.0650781371887,0.0648480619195,0.0650885009396,0.0651216649424,0.0651797019472,0.0651569016953,0.0651382469438,0.065320648959,0.0654781779722,0.0653019942075,0.065260539204,0.0654657414711,0.0652895577064,0.0655051237244,0.0656274159846,0.065726907993,0.0659238192594,0.0658243272511,0.0659030917577,0.0659694197632,0.0661497490283,0.0662119315335,0.0663362965439,0.0662596047875,0.0661684037799,0.0661352397771,0.0659404012608,0.0661746220304,0.0664150610505,0.066732191827,0.0665974630657,0.066589172065,0.0665912448152,0.0667197553259,0.0670140858505,0.0671073596083,0.0673104891253,0.0672793978727,0.0673001253744,0.0672006333661,0.0674016901329,0.0675136186423,0.0674493633869,0.0673560896291,0.067198560616,0.0669373940941,0.0670016493495,0.0669809218478,0.0668793570893,0.0668938663405,0.0668959390907,0.0667259735765,0.0668482658367,0.0671612511128,0.0671923423654,0.067594455899,0.0677768579143,0.0678887864236,0.0679675509302,0.0682598087046,0.0684380652195,0.0689065067587,0.0692174192847,0.0693334932944,0.0695469865622,0.0696713515726,0.0697542615795,0.0698599718384,0.0700962653581,0.0698620445885,0.0701045563588,0.0701957573664,0.0699615365969,0.0700423738536,0.0701149201097,0.0701874663657,0.0700299373526,0.0700610286052,0.070071392356,0.0703553591298,0.070417541635,0.0701916118661,0.0705045971422,0.0703864503824,0.0706621261554,0.0706994356585,0.0712010412004,0.0710849671907,0.0713461337126,0.0715554814801,0.0716238822358,0.0719285765113,0.0720259957694,0.0722208342857,0.0722208342857,0.0724239638027,0.0722166887853,0.0724840735577,0.0725856383162,0.0724260365528,0.072571129065,0.072859241339,0.0729504423467,0.0729815335992,0.0729400785958,0.0730602981058,0.0732883006249,0.0734541206387,0.0734458296381,0.0736759049073,0.0737816151661,0.0737463784132,0.073852088672,0.0741878742001,0.0744925684755,0.0746355882375,0.0749672282652,0.0752429040382,0.0754273788037,0.075802546585,0.0757362185795,0.0757880373338,0.0759020385933,0.0761528413643,0.0764741176411,0.0767124839111,0.0767705209159,0.0768741584246,0.0770441239388,0.0769093951775,0.077286635709,0.0774524557229,0.0775540204814,0.0773964914682,0.077442091972,0.0775146382281,0.0774545284731,0.077429655471,0.0774939107264,0.0778794422586,0.0783333745465,0.0786795238254,0.0791707656165,0.0794091318864,0.0795417878975,0.0796101886532,0.0802050679529,0.0805677992333,0.0810424590229,0.0811004960278,0.0810818412762,0.0811606057828,0.0813347167973,0.0816684295752,0.0821762533677,0.0828188059214,0.0831981192031,0.0839982007699,0.0845785708184,0.0854905808947,0.0861455699494,0.0875032213129,0.0884173041393,0.0893127322141,0.0902164512896,0.090854858343,0.0916197031569,0.0923804024705,0.0928218982574,0.0933297220498,0.093756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m <- 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ycorr <- 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altd  <- c(212)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('Tupaia_belangeri-female-liver-H3K27Ac-ERR572198.50mers.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) : 212',bty='n')
dev.off()