# R script for Peak Model
#  -- generated by MACS
p <- c(0.0287843288377,0.0336989149158,0.0386753196867,0.0434508137059,0.0479867602906,0.0481103976762,0.0480447153151,0.0481567616958,0.048519946516,0.0487672212872,0.0489217680193,0.0489294953559,0.0489835867121,0.0490260870634,0.0494704089179,0.0497524567038,0.0502122332316,0.0502547335829,0.0501156415241,0.0499997314751,0.0501504145388,0.0502895065976,0.0505058720224,0.0507686014668,0.0508961025207,0.0509270118671,0.0506874644325,0.0505020083541,0.0506874644325,0.050706782774,0.050745419457,0.0508536021694,0.0508149654864,0.0508651931743,0.050938602872,0.0510815585992,0.0514292887462,0.0518272465811,0.0516765635174,0.0518929289422,0.05235270547,0.0524763428556,0.0523990694896,0.0525767982314,0.0528086183294,0.052777708983,0.0527931636562,0.052816345666,0.0529979380761,0.0531833941546,0.0529593013931,0.0530829387787,0.0532374855108,0.0531524848082,0.0531949851595,0.053137030135,0.0532104398327,0.0534693056088,0.0534345325941,0.0536315796774,0.0538595361071,0.0543502219813,0.0547056794649,0.055119091973,0.0552388656904,0.0557256878962,0.0560231903553,0.0560000083455,0.0563825115073,0.0564791032148,0.0567225143177,0.056571831254,0.0567843330105,0.0570316077817,0.0572634278797,0.0572325185333,0.0573484285824,0.0578004777735,0.0581520715888,0.0583104819891,0.058360709677,0.058526847414,0.0585770751019,0.0586311664581,0.0587470765071,0.0584998017359,0.0585500294238,0.0586543484679,0.058283436311,0.0582679816378,0.0583413913355,0.058206162945,0.0582177539499,0.0583066183208,0.058410937365,0.0587741221852,0.0590368516296,0.0590098059515,0.0594193547913,0.0594889008208,0.0597902669482,0.060083905739,0.0602964074955,0.0606480013109,0.0607677750282,0.0610343681409,0.061254597234,0.0614516443173,0.0617800561229,0.0622977876751,0.0626493814905,0.0629468839496,0.0631632493744,0.0630782486718,0.0634530244969,0.063634616907,0.0638355276587,0.064109848108,0.0643107588596,0.0644073505671,0.0645078059429,0.0645889429772,0.0645464426259,0.0646159886553,0.064689398353,0.064816899407,0.0648903091047,0.0649791734756,0.0648284904119,0.0647473533776,0.0645618972991,0.0647589443825,0.0652071299053,0.065910317536,0.0661150919559,0.0665053224542,0.0670462360163,0.0672278284264,0.0675601039002,0.0678769247009,0.068444883941,0.0683560195701,0.0682787462041,0.068135790477,0.0683985199214,0.0685298846436,0.0686496583609,0.0683907925848,0.0685646576583,0.0687887504197,0.0689046604688,0.0691944355913,0.0694378466942,0.0696503484507,0.0697276218167,0.0699826239246,0.0696387574458,0.0701873983445,0.0702994447252,0.0706201291941,0.0706896752235,0.0710335417023,0.0714469542104,0.0716555922986,0.0720149134505,0.0722235515388,0.0728340111302,0.0731740139407,0.0734908347413,0.0735101530828,0.0736762908197,0.0739390202641,0.0741592493572,0.074271295738,0.0744760701579,0.0748353913098,0.0749435740222,0.0752835768327,0.075159939447,0.0754728965794,0.0759210821022,0.0762494939077,0.0764542683277,0.0765779057133,0.0766319970695,0.0763306309421,0.0763190399372,0.0762726759176,0.0770183638995,0.0773235936953,0.0774974587688,0.0774897314322,0.0777138241936,0.0778876892671,0.0782508740873,0.0787415599615,0.0793597468895,0.0794524749288,0.0796302036706,0.079545202968,0.0796495220121,0.0801402078862,0.0804261193404,0.0808047588339,0.0807970314973,0.080870441195,0.0809554418976,0.0816199928453,0.081732039226,0.082311589471,0.0828022753452,0.0828138663501,0.0831075051409,0.0834397806147,0.0835904636784,0.0841081952307,0.0840000125183,0.0842511509578,0.0846761544708,0.0846722908025,0.0846993364807,0.0846452451244,0.0847263821588,0.0848075191931,0.085128203662,0.0851359309986,0.0857347995852,0.0855802528531,0.0856497988825,0.0860052563662,0.0864070778694,0.0870252647975,0.0870870834903,0.0873652676079,0.087508223335,0.0880336822239,0.0884355037271,0.0888875529182,0.0893975571339,0.0895830132123,0.0895946042172,0.0901934728038,0.0904098382286,0.0908927967661,0.0911825718887,0.0915303020357,0.09161143907,0.0919012141925,0.0919128051974,0.0922064439883,0.0923378087105,0.0923687180569,0.0928169035797,0.093052587346,0.09356645523,0.0935741825666,0.0939875950747,0.0939798677381,0.0942232788411,0.0943971439146,0.0946057820028,0.0949032844619,0.0951891959161,0.0950887405403,0.0948762387838,0.0951698775746,0.0951891959161,0.0956296541024,0.0959310202298,0.0960546576154,0.0965955711775,0.0967501179095,0.0970862570516,0.0977778536774,0.0982183118636,0.0986664973865,0.0989060448211,0.0990296822067,0.0992615023047,0.0995667321005,0.099663323808,0.0997869611936,0.100169464355,0.100308556414,0.100957652689,0.100745150932,0.101096744747,0.101552657607,0.102120616847,0.102812213473,0.103256535327,0.103828358236,0.103982904968,0.10416063371,0.104264952754,0.104983595058,0.105424053244,0.105663600678,0.10606928585,0.105934057459,0.106617926749,0.106853610515,0.107243841013,0.107935437639,0.108572942909,0.109214311846,0.109828635106,0.110694096806,0.111076599967,0.11198069835,0.112382519853,0.112973661103,0.113448892304,0.113773440441,0.114306626666,0.114924813594,0.115036859975,0.1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m <- 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ycorr <- 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altd  <- c(248)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('WT_H3K4me3_5-GSM1017409.36mers.unique.MACS-2.1.0_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) : 248',bty='n')
dev.off()