# R script for Peak Model
#  -- generated by MACS
p <- c(0.0226891748807,0.0261080916435,0.0294234048681,0.0330495287075,0.0361576348555,0.0357432207025,0.0349143923963,0.0350179959346,0.0350179959346,0.0353288065494,0.0363648419321,0.0362612383938,0.0374008773148,0.037504480853,0.0372972737765,0.035950427779,0.0352252030111,0.034396374705,0.0340855640902,0.0335675463988,0.0340855640902,0.0350179959346,0.0335675463988,0.0337747534754,0.034396374705,0.0352252030111,0.0358468242407,0.0377116879296,0.0378152914678,0.0369864631617,0.0365720490086,0.0353288065494,0.0353288065494,0.0344999782433,0.0354324100877,0.0350179959346,0.0353288065494,0.032842321631,0.0331531322458,0.0336711499371,0.0333603393223,0.0336711499371,0.034396374705,0.0354324100877,0.0342927711667,0.0356396171642,0.0350179959346,0.0369864631617,0.0370900667,0.0377116879296,0.0372972737765,0.0381261020826,0.0380224985444,0.0383333091592,0.0378152914678,0.035950427779,0.0360540313173,0.0352252030111,0.0362612383938,0.0365720490086,0.0364684454703,0.0365720490086,0.0370900667,0.0364684454703,0.0379188950061,0.0403017763863,0.0415450188455,0.0410270011541,0.0406125870011,0.0404053799245,0.041752225922,0.0407161905393,0.0394729480801,0.0394729480801,0.0391621374653,0.0380224985444,0.0372972737765,0.0376080843913,0.0368828596234,0.0366756525469,0.0364684454703,0.0377116879296,0.0383333091592,0.0379188950061,0.0376080843913,0.037504480853,0.0367792560852,0.0368828596234,0.0381261020826,0.038644119774,0.0380224985444,0.0383333091592,0.0391621374653,0.0389549303888,0.0394729480801,0.0390585339271,0.0398873622332,0.0397837586949,0.0395765516184,0.0399909657715,0.0403017763863,0.0405089834628,0.0404053799245,0.0409233976159,0.0403017763863,0.0414414153072,0.041752225922,0.043306278996,0.0436170896108,0.0441351073022,0.0456891603762,0.0456891603762,0.0453783497614,0.0457927639145,0.0468287992972,0.0464143851441,0.0452747462231,0.0443423143787,0.0445495214553,0.0439279002256,0.042891864843,0.0415450188455,0.0425810542282,0.0427882613047,0.0427882613047,0.043306278996,0.0448603320701,0.045999970991,0.0463107816058,0.0477612311416,0.0487972665242,0.0511801479044,0.0510765443661,0.0521125797488,0.0523197868254,0.0538738398994,0.0538738398994,0.0534594257463,0.0523197868254,0.0516981655958,0.0515945620575,0.0505585266748,0.0513873549809,0.0508693372896,0.0521125797488,0.0509729408279,0.0508693372896,0.051801769134,0.0522161832871,0.0536666328228,0.0547026682055,0.0551170823586,0.0551170823586,0.0561531177413,0.0568783425092,0.0577071708153,0.0580179814301,0.0579143778918,0.0594684309659,0.0586396026597,0.0581215849684,0.0579143778918,0.0584323955832,0.0580179814301,0.0563603248178,0.0555314965117,0.0555314965117,0.0562567212795,0.0556351000499,0.0545990646673,0.0539774434376,0.0552206858969,0.0553242894351,0.0557387035882,0.0557387035882,0.0558423071265,0.0568783425092,0.0568783425092,0.0573963602005,0.0584323955832,0.0595720345041,0.0594684309659,0.0590540168128,0.058743206198,0.0586396026597,0.0588468097362,0.058743206198,0.0574999637388,0.057189153124,0.0570855495857,0.0557387035882,0.0543918575907,0.0549098752821,0.0554278929734,0.0565675318943,0.0558423071265,0.0561531177413,0.0562567212795,0.0564639283561,0.0556351000499,0.0550134788203,0.0555314965117,0.056049514203,0.0550134788203,0.054495461129,0.0559459106647,0.0552206858969,0.0548062717438,0.0538738398994,0.0555314965117,0.0567747389709,0.0577071708153,0.0577071708153,0.0596756380424,0.0606080698868,0.0614368981929,0.0630945548052,0.064545004341,0.0655810397237,0.0659954538767,0.0650630220323,0.0630945548052,0.0615405017312,0.0610224840399,0.0607116734251,0.0610224840399,0.061851312346,0.0607116734251,0.060297259272,0.0592612238893,0.0604008628103,0.0619549158843,0.06340536542,0.0635089689583,0.0635089689583,0.0628873477287,0.0622657264991,0.0639233831114,0.064545004341,0.0647522114175,0.0653738326471,0.0643377972645,0.0641305901879,0.0635089689583,0.0635089689583,0.0631981583435,0.0626801406522,0.0622657264991,0.0633017618818,0.0638197795731,0.0643377972645,0.0659954538767,0.0658918503385,0.0663062644915,0.0674459034125,0.0684819387952,0.0682747317186,0.0696215777161,0.0680675246421,0.0683783352569,0.0677567140273,0.0679639211038,0.0688963529482,0.0679639211038,0.0674459034125,0.0681711281804,0.0697251812544,0.0696215777161,0.0713828378667,0.071900855558,0.0736621157086,0.0737657192468,0.0737657192468,0.0748017546295,0.0753197723209,0.0743873404765,0.0746981510913,0.0748017546295,0.076148600627,0.0791531032368,0.0800855350812,0.08195039877,0.0825720199996,0.0849549013798,0.0860945403007,0.0869233686069,0.0878558004513,0.0879594039896,0.0878558004513,0.0852657119946,0.0839188659971,0.0834008483058,0.0827792270762,0.0827792270762,0.0823648129231,0.083090037691,0.0825720199996,0.0840224695354,0.084644090765,0.0852657119946,0.0855765226094,0.0865089544538,0.0884774216809,0.0878558004513,0.088891835834,0.0892026464488,0.090445888908,0.0911711136759,0.0912747172141,0.0913783207524,0.0953152552066,0.0966621012041,0.0965584976658,0.0982161542781,0.0992521896608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m <- 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ycorr <- 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altd  <- c(153)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('TBF1_rep2-GSM5884436.2x25mers.Spar+sacCer3.unique.dedup.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) : 153',bty='n')
dev.off()