# R script for Peak Model
#  -- generated by MACS
p <- c(0.0266150219962,0.0311429627778,0.0353321993278,0.0395392624163,0.0437998051203,0.0438532847358,0.0436393662737,0.0434432743501,0.0436750193507,0.0434611008886,0.0434611008886,0.0430867435799,0.0431223966569,0.0433897947345,0.0431937028109,0.042498467809,0.042498467809,0.0417141001146,0.0415180081909,0.0415001816524,0.0412327835748,0.0413219162673,0.0417497531916,0.0414288754984,0.0412506101133,0.041696273576,0.0412684366518,0.0422667228084,0.0419814981922,0.0423023758854,0.0425519474245,0.0426410801171,0.0419814981922,0.0419993247307,0.0423380289624,0.0420706308848,0.0426232535786,0.0418923654997,0.0418388858841,0.0415714878065,0.041696273576,0.0418745389611,0.0417854062686,0.0419280185767,0.0422667228084,0.042391508578,0.042462814732,0.0428549985792,0.0430332639643,0.0429441312718,0.0426410801171,0.0423558555009,0.0426410801171,0.042498467809,0.0422132431928,0.0421954166543,0.0421775901158,0.0428371720407,0.0426945597326,0.0429619578103,0.0431223966569,0.0436037131967,0.043371968196,0.0432115293494,0.0427836924252,0.042391508578,0.0430154374258,0.0419993247307,0.0422488962699,0.0423023758854,0.0422310697314,0.0416427939605,0.0419993247307,0.0419636716537,0.0424806412705,0.0427658658867,0.0420349778077,0.0423558555009,0.0426054270401,0.0423023758854,0.0422488962699,0.042391508578,0.0424806412705,0.0426945597326,0.0425162943475,0.0424449881935,0.0426767331941,0.0428015189637,0.0426589066556,0.0424093351165,0.0429976108873,0.0429797843488,0.0426589066556,0.0426945597326,0.0433184885805,0.0434432743501,0.0429976108873,0.0431402231954,0.0431758762724,0.0435680601196,0.0432828355035,0.043336315119,0.0436215397352,0.0437998051203,0.0428549985792,0.0430689170414,0.0435858866582,0.0435145805041,0.0436750193507,0.0435324070426,0.0434789274271,0.0435680601196,0.0435680601196,0.0438354581973,0.0444772135837,0.0444950401222,0.044174162429,0.0439780705054,0.044209815506,0.0442632951216,0.044209815506,0.0443346012756,0.0443880808911,0.0440672031979,0.0441563358905,0.0438711112743,0.0439245908899,0.0442632951216,0.0443702543526,0.0448515708924,0.0447802647384,0.0447624381998,0.0448515708924,0.0449585301235,0.0447267851228,0.0452615812781,0.0455111528173,0.0451546220471,0.0445306931992,0.0439067643513,0.0444950401222,0.0443880808911,0.0442811216601,0.0446554789688,0.0447802647384,0.0445841728147,0.0448337443539,0.0450654893545,0.0452615812781,0.0457785508949,0.0451189689701,0.0452437547396,0.0455111528173,0.0452081016626,0.0452972343552,0.0458320305105,0.0457607243564,0.0459389897415,0.0459568162801,0.0456181120484,0.0463668266658,0.0464024797428,0.0462420408962,0.046687704359,0.0468303166671,0.0469016228211,0.0470620616677,0.0467411839745,0.0470977147447,0.0475790312845,0.0474007658994,0.0475077251305,0.047489898592,0.046759010513,0.0473116332068,0.0469907555137,0.0463133470503,0.0467411839745,0.0468124901286,0.0470442351292,0.0470085820522,0.0470264085907,0.0471690208988,0.047561204746,0.0471333678217,0.0472759801298,0.0480781743628,0.0482564397479,0.0484525316715,0.0482207866709,0.0476681639771,0.0476859905156,0.0479533885932,0.0476503374385,0.0478286028237,0.0476681639771,0.0473651128224,0.0469907555137,0.0465094389739,0.0461350816652,0.046759010513,0.0465629185894,0.0462420408962,0.0466698778205,0.0465272655124,0.0464024797428,0.0463311735888,0.046652051282,0.0468303166671,0.0474364189764,0.0478642559007,0.0479533885932,0.0479712151317,0.0478464293622,0.0477038170541,0.0476146843615,0.0477216435926,0.0474007658994,0.0473472862839,0.0468124901286,0.0466698778205,0.0472938066683,0.0471868474373,0.0476325109,0.0479177355162,0.0484881847485,0.0487912359032,0.0490586339809,0.049272552443,0.0500034405219,0.050074746676,0.0498608282138,0.0501995324455,0.0498964812909,0.0497538689828,0.0494508178281,0.0495042974436,0.0497538689828,0.0498251751368,0.04930820552,0.0494508178281,0.0498251751368,0.050074746676,0.0501995324455,0.0504669305232,0.0508769409089,0.0508056347549,0.0504669305232,0.0504134509077,0.0508412878319,0.0504134509077,0.0500925732145,0.05014605283,0.0505917162928,0.051019553217,0.0508947674475,0.0507699816779,0.0512334716792,0.0514830432183,0.051750441296,0.0517682678345,0.0522852374513,0.0518752270655,0.0519108801426,0.0517326147575,0.0518039209115,0.0529448193762,0.0531765643768,0.0533904828389,0.0530339520687,0.0536935339936,0.0533191766849,0.0543887689955,0.0543174628415,0.0542818097645,0.0549592182278,0.0542639832259,0.0546026874576,0.0548522589968,0.0552622693825,0.0555296674602,0.0556901063068,0.0554405347676,0.0552622693825,0.0553870551521,0.0549057386123,0.0545135547651,0.0545135547651,0.0549413916893,0.0548166059198,0.0549057386123,0.0554405347676,0.0556366266912,0.0561535963081,0.0563140351546,0.0567775251559,0.0576688520814,0.0575975459274,0.0578471174665,0.0580966890057,0.0579719032361,0.057793637851,0.0579897297746,0.0585423524685,0.0587384443921,0.0587206178536,0.0590414955468,0.0592197609319,0.0591484547778,0.0599149959338,0.0606637105512,0.0604319655506,0.0608241493978,0.0607706697823,0.06144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m <- 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ycorr <- 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altd  <- c(135)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('96-LFY-GSE64245/p35S-LFY-rep2-GSM1566965/all.1x36mers.TAIR10.unique.MACS2_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) : 135',bty='n')
dev.off()