# R script for Peak Model
#  -- generated by MACS
p <- c(0.0344480859486,0.0404708595027,0.0462057226931,0.0521039944684,0.0576054168234,0.0574809150445,0.0577532626858,0.058017828966,0.058663681944,0.0586948073887,0.0587025887499,0.0585936496934,0.0585469615263,0.0582823952461,0.0586169937769,0.0587726210006,0.0590138431972,0.0593328790056,0.0588893414183,0.0580722984943,0.0572941623762,0.0575431659339,0.0575509472951,0.058017828966,0.0587025887499,0.058920466863,0.0591305636149,0.0592706281161,0.0587881837229,0.0590449686419,0.0601810473743,0.05982310476,0.0601732660131,0.0601732660131,0.0597063843423,0.0597452911482,0.0596674775364,0.0588582159735,0.0592317213102,0.0596130080081,0.059651914814,0.0597219470646,0.059994294706,0.0598620115659,0.0598620115659,0.0600254201507,0.0600721083178,0.0608346817135,0.0609202766865,0.0612548752173,0.0614727533304,0.0614727533304,0.0612159684114,0.061068122549,0.0607879935465,0.0607490867405,0.0607724308241,0.0613560329127,0.0618540400283,0.0609903089372,0.0607724308241,0.0612159684114,0.0612704379397,0.0611692802443,0.0619318536401,0.0616906314435,0.0615816923869,0.0604767390992,0.0605234272663,0.060896932603,0.060982527576,0.0610992479937,0.0609358394089,0.0612548752173,0.0610759039101,0.06081133763,0.0610369971042,0.0620174486131,0.0617995705,0.0618696027506,0.0618462586671,0.0618073518612,0.0618306959447,0.0615894737481,0.0612315311338,0.061713975527,0.0614649719692,0.0607802121853,0.060251079625,0.0604923018216,0.0603055491532,0.0602355169026,0.0606712731287,0.0611148107161,0.0614494092468,0.0622508894485,0.0621108249472,0.0623987353109,0.0634258749868,0.0636359717387,0.0639783516307,0.0637915989623,0.0636593158223,0.0635737208493,0.0633402800138,0.0624998930063,0.0627488965641,0.0631846527902,0.0628500542594,0.0627800220088,0.0622897962544,0.0626788643134,0.0631146205396,0.0631146205396,0.0632702477632,0.0634103122645,0.063604846294,0.0634025309033,0.0637838176012,0.0635970649328,0.0639550075471,0.0635036885986,0.063262466402,0.0635114699598,0.0636359717387,0.0641339788543,0.0645619537193,0.0644530146627,0.0639861329919,0.0642973874391,0.0644530146627,0.0650443981125,0.0654412475327,0.0657447206188,0.0657135951741,0.0661337886778,0.0655346238669,0.0657135951741,0.0662660718179,0.0666162330711,0.0664995126533,0.0663438854297,0.0664450431251,0.0668418925453,0.0672776487715,0.0670053011301,0.0673554623833,0.0678845949436,0.0677134049976,0.0676511541081,0.0678301254153,0.0678456881377,0.0674877455233,0.0671375842702,0.0674254946339,0.0675110896069,0.0676278100246,0.0671687097149,0.0672076165208,0.0669663943242,0.0668574552677,0.067472182801,0.0674799641622,0.0675811218575,0.0668185484618,0.0673554623833,0.0671453656314,0.0676900609141,0.0682191934744,0.0690907059266,0.0700789387966,0.0696120571258,0.0700011251848,0.0703435050768,0.0704835695781,0.0698532793224,0.0704913509392,0.0700867201578,0.0698766234059,0.0692463331503,0.0684215088651,0.0683903834203,0.0689895482313,0.0682970070862,0.0688183582853,0.06884948373,0.0685071038381,0.0682114121132,0.0686860751452,0.068763888757,0.0692463331503,0.0695887130422,0.0685226665604,0.0688883905359,0.0689584227866,0.0694019603739,0.0693085840397,0.0701956592144,0.0695031180692,0.0693863976515,0.0690984872878,0.069277458595,0.0698143725165,0.0697676843494,0.0694253044574,0.0693708349292,0.0694953367081,0.0694253044574,0.0699933438236,0.0695420248751,0.0693786162903,0.0687483260347,0.0684993224769,0.0684370715874,0.0684448529486,0.0685382292828,0.0686705124229,0.0689895482313,0.0693163654009,0.0701178456025,0.0709348885266,0.0720320604531,0.0721954690379,0.0721643435932,0.0724289098733,0.0725222862075,0.0724211285121,0.0719620282025,0.0721020927037,0.0719698095636,0.0716352110328,0.0706781036076,0.0705536018287,0.0710360462219,0.0708337308312,0.0709193258042,0.071168329362,0.0703979746051,0.0697209961823,0.070008906546,0.0699622183789,0.0709660139713,0.0711449852784,0.0707559172194,0.0714873651704,0.071168329362,0.0715029278928,0.0725300675687,0.0724444725957,0.0725689743746,0.0727712897653,0.0729502610724,0.0732537341585,0.0736583649399,0.0728802288218,0.0729969492395,0.0729658237948,0.0727712897653,0.0725378489299,0.0725300675687,0.0726545693476,0.0720009350084,0.0719698095636,0.0721876876767,0.0726856947923,0.0731525764632,0.0727090388758,0.0728802288218,0.0734638309104,0.0731992646302,0.0727712897653,0.072973605156,0.0726234439028,0.0725534116522,0.0719698095636,0.0720320604531,0.0730202933231,0.0729891678784,0.0726545693476,0.0729269169889,0.0732848596032,0.0731136696573,0.0735494258834,0.0741252466108,0.0753469203162,0.0752846694268,0.0750590099525,0.075424733928,0.0760394614613,0.0758838342377,0.0764907804098,0.0760005546554,0.0759538664883,0.0759227410436,0.0759772105719,0.0757359883753,0.0753313575939,0.0758838342377,0.076241776852,0.0773622928621,0.0785995292899,0.0816731669564,0.0842098907014,0.0872757470068,0.0895945926387,0.092613760777,0.0964655345616,0.0987299106653,0.101523419329,0.104698214691,0.106480146402,0.107592881051,0.108347673085,0.108223171306,0.1089312751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m <- 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ycorr <- 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altd  <- c(216)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('LUC-NSD2-vs-LUC-IgG.2x25mers.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) : 216',bty='n')
dev.off()