# R script for Peak Model
#  -- generated by MACS
p <- c(0.0184895057303,0.0214399587723,0.0247838055533,0.0277342585954,0.0308814085069,0.0310781053764,0.0306847116375,0.0296028788554,0.0295045304206,0.0284226976386,0.0287177429428,0.0287177429428,0.0287177429428,0.0287177429428,0.0282260007691,0.029012788247,0.0296028788554,0.030488014768,0.0313731506806,0.0328483772017,0.0315698475501,0.0321599381585,0.031963241289,0.0320615897238,0.0329467256364,0.0322582865932,0.0324549834627,0.0328483772017,0.0321599381585,0.0315698475501,0.0329467256364,0.0327500287669,0.0331434225059,0.0344219521574,0.0339302099837,0.0355037849395,0.0354054365048,0.0361922239827,0.0378641473732,0.0379624958079,0.0367823145911,0.0368806630258,0.0364872692869,0.0359955271132,0.0369790114605,0.0365856177216,0.0363889208521,0.0362905724174,0.0361922239827,0.0368806630258,0.0387492832858,0.0388476317205,0.0398311160679,0.0403228582415,0.0389459801553,0.0383558895468,0.0393393738942,0.0382575411121,0.0385525864163,0.0380608442426,0.0373724051995,0.0372740567647,0.0372740567647,0.0370773598953,0.0379624958079,0.0397327676331,0.0394377223289,0.0406179035458,0.0398311160679,0.0398311160679,0.0401261613721,0.0403228582415,0.0410112972847,0.0417980847626,0.0439617503268,0.0426832206752,0.0425848722405,0.0420931300668,0.0417980847626,0.0429782659794,0.0429782659794,0.0431749628489,0.0429782659794,0.0427815691099,0.0407162519805,0.0416013878931,0.0410112972847,0.0406179035458,0.0424865238057,0.0420931300668,0.0418964331973,0.0421914785015,0.042388175371,0.042388175371,0.0425848722405,0.0434700081531,0.0445518409352,0.0455353252825,0.0446501893699,0.0458303705867,0.0468138549341,0.0476989908467,0.0481907330204,0.0475022939772,0.0480923845857,0.0464204611951,0.0466171580646,0.0470105518036,0.0482890814551,0.0480923845857,0.0481907330204,0.0488791720635,0.0491742173677,0.0500593532804,0.0498626564109,0.0512395344972,0.0508461407582,0.0483874298899,0.0485841267593,0.0485841267593,0.0487808236288,0.0485841267593,0.0483874298899,0.0482890814551,0.0496659595414,0.049075868933,0.0508461407582,0.0531081547572,0.0515345798014,0.0519279735403,0.0508461407582,0.0508461407582,0.0503543985846,0.0511411860625,0.050551095454,0.0521246704098,0.0513378829319,0.0508461407582,0.0508461407582,0.050551095454,0.0510428376277,0.0514362313667,0.0523213672793,0.0515345798014,0.0521246704098,0.0527147610182,0.0527147610182,0.0550751234519,0.0563536531034,0.0558619109298,0.0571404405813,0.0563536531034,0.0559602593645,0.0570420921466,0.0572387890161,0.0569437437118,0.0575338343203,0.0568453952771,0.0584189702329,0.0597958483192,0.0592057577108,0.0599925451886,0.0610743779707,0.0607793326665,0.0615661201444,0.0614677717097,0.0611727264055,0.0600908936234,0.0599925451886,0.059107409276,0.0581239249287,0.0580255764939,0.0575338343203,0.0578288796245,0.057632182755,0.0582222733634,0.0584189702329,0.059107409276,0.0582222733634,0.0584189702329,0.0600908936234,0.0598941967539,0.0595991514497,0.059107409276,0.0592057577108,0.0583206217981,0.0584189702329,0.0582222733634,0.0577305311897,0.0585173186676,0.0584189702329,0.0587140155371,0.0594024545802,0.059500803015,0.0584189702329,0.0575338343203,0.0588123639718,0.0600908936234,0.0616644685792,0.0623529076223,0.0648116184907,0.0658934512728,0.0660901481422,0.0671719809243,0.0682538137064,0.0714993120527,0.0693356464885,0.0683521621412,0.0660901481422,0.0654017090991,0.0631396951002,0.0623529076223,0.0608776811013,0.0621562107528,0.0622545591876,0.0603859389276,0.062844649796,0.0642215278823,0.0665818903159,0.0673686777938,0.0671719809243,0.0683521621412,0.0700240855317,0.0683521621412,0.0690406011843,0.0707125245748,0.0687455558801,0.0674670262285,0.0659917997075,0.0653033606644,0.0655984059686,0.0651066637949,0.0637297857086,0.0641231794475,0.0627463013612,0.0602875904929,0.0617628170139,0.0632380435349,0.0636314372739,0.0642215278823,0.065795102838,0.0655000575338,0.0672703293591,0.0689422527496,0.0699257370969,0.0732695838779,0.0737613260516,0.0720894026611,0.0726794932695,0.0730728870085,0.0736629776169,0.0742530682253,0.0754332494421,0.0755315978769,0.0754332494421,0.0745481135295,0.0753349010074,0.0764167337895,0.0763183853547,0.0772035212674,0.0768101275284,0.0753349010074,0.0739580229211,0.0732695838779,0.0733679323127,0.0724827964001,0.071400963618,0.0705158277053,0.0715976604874,0.0708108730096,0.0704174792706,0.0714993120527,0.0719910542264,0.0724827964001,0.072876190139,0.0722860995306,0.072876190139,0.0746464619642,0.07435141666,0.0738596744864,0.0738596744864,0.0755315978769,0.0744497650948,0.0741547197906,0.0760233400505,0.077695263441,0.0787770962231,0.0794655352663,0.0802523227442,0.0816292008305,0.0831044273515,0.0823176398736,0.0831044273515,0.0831044273515,0.0815308523957,0.0813341555262,0.0808424133526,0.0788754446579,0.0791704899621,0.0783837024842,0.0775969150063,0.0788754446579,0.0796622321357,0.0804490196136,0.0821209430041,0.082907730482,0.0857598350893,0.0885135912619,0.0871367131756,0.0885135912619,0.0888086365661,0.0887102881314,0.091464044304,0.09244752865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m <- 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ycorr <- 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altd  <- c(140)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('MYOD-FLAG_ChIP_dox+_ctrl_SA-tTA-MyoD_ESCs-GSM2576038/SRR5445217.36mers.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) : 140',bty='n')
dev.off()