# R script for Peak Model
#  -- generated by MACS
p <- c(0.0239595412609,0.0280832967285,0.031841656142,0.035182420065,0.038679782297,0.0387580814515,0.0378967907526,0.0382360870885,0.0387580814515,0.0380011896252,0.0380272893433,0.0379489901889,0.03779239188,0.0380011896252,0.03779239188,0.0374269958259,0.0377401924437,0.0375574944166,0.0363830070999,0.0369050014629,0.0371137992081,0.0364613062544,0.0368267023084,0.0374008961077,0.0376357935711,0.0375835941348,0.0375574944166,0.0382621868066,0.0383926853974,0.0388102808878,0.0387841811696,0.0393583749689,0.0389146797604,0.0388102808878,0.0386014831426,0.0383665856792,0.0380011896252,0.0375835941348,0.0382360870885,0.0378967907526,0.0377401924437,0.0377662921618,0.0387580814515,0.0382360870885,0.0389407794785,0.0393322752508,0.0399586684863,0.0392539760963,0.0386014831426,0.0386536825789,0.0389146797604,0.0388363806059,0.0379489901889,0.0388102808878,0.03849708427,0.0384448848337,0.0379489901889,0.0386014831426,0.0382621868066,0.0377401924437,0.0370355000536,0.0367745028721,0.0371659986444,0.0367223034358,0.0365396054088,0.0367223034358,0.0372442977988,0.0376357935711,0.0384709845518,0.0384448848337,0.0399586684863,0.0397759704593,0.0399847682045,0.0396454718685,0.040428463413,0.0404545631312,0.0405067625675,0.0400369676408,0.0395671727141,0.0394105744052,0.0383404859611,0.03920177666,0.0392278763782,0.039723771023,0.0392800758145,0.0392278763782,0.0385492837063,0.0386275828607,0.0393583749689,0.0401674662315,0.0404806628493,0.0405328622856,0.0402718651041,0.040767759749,0.040950457776,0.0411592555212,0.0417073496023,0.041994446502,0.0420205462201,0.0419683467838,0.0420988453746,0.0411853552393,0.0410287569305,0.040767759749,0.0410026572123,0.0411331558031,0.0407938594671,0.0406372611582,0.0402718651041,0.0405328622856,0.0405589620038,0.0416290504479,0.0416290504479,0.0414202527027,0.0411331558031,0.0410548566486,0.040950457776,0.0414202527027,0.0417073496023,0.041472452139,0.0415507512934,0.0414202527027,0.0420727456564,0.0423859422742,0.0424903411468,0.0428296374827,0.0431689338187,0.0431689338187,0.0428296374827,0.0427513383283,0.0426730391738,0.0424381417105,0.0424642414287,0.0427513383283,0.0433255321276,0.0439780250813,0.0445000194443,0.0441346233902,0.044630518035,0.0449176149347,0.045674506761,0.0458311050699,0.0455701078884,0.0454396092977,0.0451786121162,0.0450220138073,0.0448654154984,0.0452308115525,0.0452047118343,0.0448132160621,0.0445522188806,0.0447349169076,0.044630518035,0.0448915152165,0.0451786121162,0.0442912216991,0.0437170278998,0.0432472329731,0.043403831282,0.0441346233902,0.0443434211354,0.0446827174713,0.045152512398,0.0451786121162,0.0451786121162,0.0455962076066,0.0469533929503,0.04794518224,0.0481539799852,0.0483105782941,0.0480756808307,0.0479712819581,0.0483888774485,0.0482061794215,0.0479973816763,0.0479712819581,0.0473970881588,0.0472926892862,0.0478407833674,0.048127880267,0.0484149771667,0.0486237749119,0.0483366780122,0.0485976751937,0.0491196695567,0.0490674701204,0.0492501681474,0.0496155642015,0.0494850656108,0.049171868993,0.0494589658926,0.0492240684293,0.0499809602556,0.050398555746,0.0504246554641,0.0513642453175,0.0518862396805,0.0521211371438,0.0524082340435,0.0525126329161,0.0527214306613,0.0532173253061,0.0525909320705,0.0531129264335,0.0531651258698,0.052669231225,0.0522516357346,0.0518340402442,0.0517557410898,0.0520428379894,0.0520950374257,0.0524082340435,0.0527736300976,0.0520689377075,0.0528780289702,0.0539220176961,0.0546789095225,0.0549921061402,0.0549921061402,0.0551748041673,0.0556967985303,0.0556184993758,0.0564797900747,0.0569495850014,0.0571583827466,0.0567929866925,0.0573410807737,0.0578369754185,0.0571844824648,0.0584633686541,0.0586721663993,0.0592985596349,0.0590375624534,0.059141961326,0.05880266499,0.0587765652719,0.0584894683722,0.0585155680904,0.0601337506156,0.0596639556889,0.059324659353,0.059141961326,0.0593507590712,0.0600032520249,0.0603164486427,0.061073340469,0.061778032859,0.0619868306042,0.0614909359594,0.0609167421601,0.0612299387779,0.0621956283494,0.0622478277857,0.0629264204576,0.0628742210213,0.0636311128476,0.0627176227124,0.063344015948,0.0636833122839,0.0652492953729,0.0655885917088,0.065797389454,0.0667369793074,0.0664237826896,0.0675721702881,0.0674677714155,0.0691903528134,0.0689293556319,0.0698950452034,0.069477449713,0.0699733443579,0.0702865409756,0.0703648401301,0.0709390339294,0.0707563359023,0.0708085353386,0.0710173330838,0.0719830226553,0.0715915268831,0.0715132277287,0.0720091223735,0.0718786237827,0.0725311167365,0.0730792108176,0.072792113918,0.0733402079991,0.0724267178639,0.0732097094083,0.0755064846055,0.0763416755862,0.0766026727677,0.0774117640304,0.0776205617756,0.0785340519108,0.0793692428915,0.0803349324631,0.0819531149883,0.0814833200616,0.0814572203435,0.0819270152702,0.082422909915,0.0826839070965,0.0832581008958,0.0827361065328,0.083832294695,0.0843803887762,0.0862334687648,0.0877211526993,0.0873818563633,0.0891566371975,0.0893915346608,0.0903311245142,0.0906182214138,0.0916622101398,0.0915839109853,0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m <- 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ycorr <- 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altd  <- c(225)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('A549-100nM-Dex-1h-p300.pooled.sorted.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) : 225',bty='n')
dev.off()