# R script for Peak Model
#  -- generated by MACS
p <- c(0.0317699534232,0.0369693681832,0.0430672112289,0.0478078540983,0.0538865816486,0.0542115450711,0.0557790156973,0.0543262380437,0.0547850099343,0.054899702907,0.0553011283112,0.0547658944389,0.0544409310164,0.0547658944389,0.0544791620073,0.0532748857945,0.0510192573324,0.0507325249008,0.0495855951743,0.0478652005846,0.0476166991439,0.0473681977032,0.046106575004,0.0474637751804,0.0465844623901,0.0459154200496,0.0462212679767,0.0458389580679,0.0470623497761,0.0481137020254,0.0486680513932,0.0489547838248,0.0494135557154,0.0472152737396,0.0464315384265,0.0467182708582,0.0461448059949,0.0467756173445,0.0470432342807,0.0472343892351,0.0463741919402,0.0460683440132,0.0466800398673,0.0468138483354,0.0473681977032,0.0478269695937,0.0485915894114,0.0488974373385,0.0476166991439,0.0476358146393,0.0474637751804,0.0474446596849,0.0463359609493,0.0460301130223,0.0462212679767,0.045456648159,0.0451316847365,0.0444626423961,0.0448258368095,0.0437362535693,0.0445199888824,0.0445391043779,0.0456095721226,0.0453419551864,0.0452272622138,0.0456478031135,0.0453419551864,0.0448640678004,0.0444817578915,0.0453993016727,0.0456095721226,0.0449596452776,0.0432392506879,0.0442714874417,0.043850946542,0.0434877521286,0.0435450986149,0.044978760773,0.0452654932046,0.0443479494235,0.0444052959098,0.0448449523049,0.0449596452776,0.0448258368095,0.0449596452776,0.0444626423961,0.044672912846,0.0434112901468,0.0433921746514,0.0437553690648,0.0428951717699,0.0424746308702,0.0435450986149,0.0439274085238,0.0438891775329,0.0439847550101,0.0440994479827,0.0448449523049,0.0451890312229,0.0454375326636,0.0521088405726,0.0538483506577,0.0550717423659,0.0564671735331,0.059927078208,0.0620680136974,0.0631575969375,0.0657381888221,0.0661204987309,0.0663498846762,0.0622973996427,0.0650117999953,0.0645530281047,0.0637884082871,0.0615901263114,0.0635781378372,0.0655279183722,0.0638839857643,0.0637692927917,0.0661778452172,0.0651647239589,0.0626414785606,0.065126492968,0.0640942562142,0.0639795632415,0.0603667346031,0.056199556597,0.0553584747976,0.0560466326334,0.0534086942626,0.0521470715634,0.0534660407489,0.0491841697701,0.0490121303111,0.0497385191379,0.0502928685057,0.0510957193142,0.050656062919,0.0494709022017,0.0498914431014,0.0496811726515,0.0469667722989,0.0475975836485,0.0474828906758,0.0465844623901,0.0464697694174,0.0462403834721,0.0471579272533,0.0470050032898,0.0462977299585,0.0464888849129,0.0464315384265,0.0463359609493,0.0470623497761,0.0465271159037,0.0459345355451,0.0464888849129,0.0461830369858,0.0461256904995,0.0464888849129,0.0463168454539,0.0471579272533,0.047272620226,0.0468520793262,0.0463168454539,0.0476549301348,0.0476358146393,0.0468138483354,0.047272620226,0.0479990090527,0.0481710485117,0.0477696231074,0.0483048569798,0.0488209753567,0.0489165528339,0.0473873131986,0.0476549301348,0.048056355539,0.0475975836485,0.0478843160801,0.0481519330162,0.0486680513932,0.0476549301348,0.0481901640071,0.0494709022017,0.0505031389555,0.0515353757093,0.052605843454,0.0531984238127,0.0522617645361,0.0526823054358,0.0528161139039,0.0530263843537,0.0525484969677,0.0522044180498,0.0518029926455,0.0505604854418,0.049700288147,0.0495091331926,0.0498340966151,0.0491077077883,0.0489547838248,0.050178175533,0.0505222544509,0.0494135557154,0.048878321843,0.0486107049068,0.0496620571561,0.0496811726515,0.0494900176971,0.0508663333689,0.0512104122868,0.0502928685057,0.049528248688,0.0506178319282,0.052605843454,0.0530263843537,0.0524338039951,0.0537527731805,0.0541541985848,0.0540012746212,0.0538674661531,0.0542688915574,0.0548041254298,0.0551099733568,0.0537910041714,0.0542115450711,0.0542688915574,0.0526823054358,0.0547658944389,0.0551290888523,0.0544600465118,0.0549188184024,0.0549952803842,0.0544409310164,0.0561804411015,0.0555113987611,0.0566009820012,0.058149337132,0.0577670272231,0.0573656018189,0.0598123852353,0.0616092418068,0.0615518953205,0.0619342052293,0.0632722899102,0.0648588760318,0.0644383351321,0.0636163688281,0.0629855574786,0.0633105209011,0.0610740079345,0.0591624583903,0.0596785767673,0.0608446219892,0.0591815738858,0.0591624583903,0.0598888472171,0.0602520416305,0.0604623120803,0.0612078164025,0.0631384814421,0.0629855574786,0.0632531744148,0.0626032475698,0.062354746129,0.0624312081108,0.0611695854117,0.0624312081108,0.0627752870287,0.063998678737,0.0634060983783,0.0640751407187,0.0635781378372,0.0648588760318,0.0639413322506,0.0654132253996,0.0662734226945,0.0657190733267,0.0653558789133,0.0635016758555,0.0635399068464,0.0654705718859,0.0656999578312,0.0646677210774,0.0661969607127,0.0648397605364,0.0654514563905,0.0659293437765,0.0653176479224,0.0659293437765,0.0656808423358,0.0648397605364,0.0655852648586,0.0674968144027,0.0672865439528,0.0676688538617,0.068376127193,0.0679173553024,0.068204087734,0.0673630059346,0.06998182881,0.0693701329559,0.0699244823237,0.0686628596246,0.0694657104331,0.0693510174605,0.0678217778252,0.0689304765608,0.0703067922325,0.0724668432174,0.0710522965547,0.072753575649,0.0731932320441,0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m <- 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ycorr <- 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altd  <- c(66, 517)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('/oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/datasets-Drosophila-ENCODE-PAS-DNAse-dm3/S2-DNAse-UW-ENCFF005BHD/S2-DNAse-UW-ENCFF005BHD.36mers.unique.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) : 66,517',bty='n')
dev.off()