# R script for Peak Model
#  -- generated by MACS
p <- c(0.0251277516264,0.0297906333715,0.0338706548985,0.0380154386719,0.0425811770474,0.0425811770474,0.0418364112131,0.042386890308,0.0422249846918,0.0421278413221,0.0420954601989,0.0421926035686,0.0427107015403,0.0431316561423,0.04280784491,0.0430668938958,0.0433907051281,0.0439088030998,0.0441354709624,0.0448154745502,0.0450745235361,0.0449773801664,0.0446859500573,0.0443297577018,0.0443297577018,0.0443297577018,0.043941184223,0.0438116597301,0.043520229621,0.0430345127726,0.0432611806352,0.042678320417,0.0431964183887,0.043520229621,0.0434878484978,0.0439735653462,0.0451716669057,0.0455926215077,0.0457221460007,0.0462402439723,0.0462402439723,0.0464669118349,0.0452688102754,0.0451392857825,0.0460135761097,0.0464992929582,0.04591643274,0.0460783383562,0.0455602403845,0.0453659536451,0.0453335725219,0.0458192893703,0.0469526286834,0.0478269190106,0.0474059644086,0.0471469154228,0.0482478736126,0.0483450169823,0.0491221639398,0.0496078807882,0.0497050241579,0.0491221639398,0.0491869261863,0.048442160352,0.0487983527075,0.0487012093378,0.0483126358591,0.0482802547358,0.0482802547358,0.0479564435035,0.0470821531763,0.0474707266551,0.0485069225984,0.0499640731438,0.0499640731438,0.0498021675276,0.0493488318024,0.0491869261863,0.049154545063,0.0490574016933,0.0506440767316,0.0510002690871,0.0503850277458,0.0494783562953,0.0503202654993,0.0507412201013,0.0502555032528,0.0507736012245,0.0514536048124,0.0513564614427,0.0510974124568,0.0513240803194,0.050838363471,0.0514212236891,0.0512916991962,0.0508707445942,0.0518097971679,0.0511945558265,0.0507736012245,0.051259318073,0.0510974124568,0.0509678879639,0.0516155104285,0.0510650313336,0.0504497899922,0.0508059823478,0.0505469333619,0.050417408869,0.0511621747033,0.0507736012245,0.0500612165135,0.0503526466225,0.0506116956084,0.0510974124568,0.0513888425659,0.051680272675,0.0518745594143,0.0516155104285,0.050838363471,0.0511297935801,0.0515831293053,0.0520364650305,0.0511621747033,0.0507412201013,0.0510002690871,0.0509678879639,0.0519393216608,0.0522631328931,0.0514859859356,0.0517126537982,0.0531698043435,0.0527812308648,0.0534288533294,0.0533317099597,0.0532669477132,0.0530726609738,0.0524574196325,0.0523602762628,0.0535907589455,0.0537526645617,0.0537850456849,0.0539145701778,0.0549831472444,0.0554041018464,0.055630769709,0.0554688640929,0.0554688640929,0.0561488676807,0.0561812488039,0.0561812488039,0.0550155283676,0.0544650492727,0.0534612344526,0.0538174268081,0.0536231400688,0.0538498079314,0.0532669477132,0.0535907589455,0.053655521192,0.0533964722061,0.0529755176042,0.0533640910829,0.052813611988,0.0526193252486,0.0531374232203,0.0535583778223,0.0541412380404,0.0545298115192,0.054918384998,0.0548212416283,0.0562460110504,0.0565698222827,0.0566022034059,0.0565698222827,0.0566669656524,0.057314588117,0.0578650672119,0.057606018226,0.0568288712685,0.0574764937331,0.0569907768847,0.0570879202544,0.0572174447473,0.0576383993493,0.0570555391311,0.0570231580079,0.0572822069937,0.0578326860886,0.0585126896765,0.0592250743875,0.0595488856198,0.0600346024683,0.0610384172884,0.0617831831227,0.0623336622176,0.062527948957,0.0616212775065,0.0611355606581,0.0614593718904,0.0610707984116,0.0617184208762,0.0610060361652,0.0606174626864,0.0598403157289,0.0600669835915,0.0596784101128,0.0612974662743,0.0617184208762,0.060973655042,0.0613946096439,0.0609088927955,0.0613946096439,0.0620422321085,0.061686039753,0.0606822249329,0.0605850815632,0.0605203193167,0.0603584137006,0.0613622285207,0.0616536586298,0.0614269907672,0.0618479453692,0.0614917530136,0.0622365188479,0.0625927112034,0.0632727147913,0.0623660433408,0.0629165224357,0.0627546168196,0.0621393754782,0.0634670015307,0.0639203372559,0.0646003408437,0.0650860576922,0.0651508199386,0.0642117673649,0.065345106678,0.0652155821851,0.0649889143225,0.0655393934174,0.0645679597205,0.0643089107346,0.0644384352276,0.0643089107346,0.065345106678,0.0653774878012,0.064503197474,0.0642441484882,0.0655070122941,0.0655393934174,0.0662517781284,0.0652479633083,0.0651184388154,0.0650860576922,0.0649565331992,0.0663813026213,0.0671260684556,0.0676765475505,0.0667698761001,0.0673527363182,0.0675146419344,0.0681946455222,0.0687127434939,0.0687451246171,0.0684213133848,0.0682917888919,0.0672879740718,0.0673527363182,0.0683241700151,0.0686156001242,0.0683565511384,0.0681298832758,0.0669641628395,0.067741309797,0.0673851174415,0.068162264399,0.0690689358494,0.0692308414656,0.0691013169727,0.0683889322616,0.0689070302333,0.0703965619019,0.0718537124472,0.0725984782815,0.0738289609642,0.073375625239,0.0744442023056,0.0736994364713,0.0740880099501,0.0755775416186,0.0760956395903,0.0762899263297,0.0764842130691,0.0750918247702,0.075059443647,0.0757070661116,0.0749946814005,0.0758042094813,0.0758689717277,0.0751889681399,0.0750918247702,0.0775204090124,0.0795604197759,0.0818918606485,0.0846766372463,0.0882385608015,0.0934195405183,0.0973052753059,0.100122433027,0.102518636146,0.105044363758,0.105789129592,0.107278661261,0.109059623038,0.1103548679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m <- 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ycorr <- 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altd  <- c(208)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('GSE46663-LY1_BCL6_DMSO-GSM1133657.36mers.unique.dedup.pseudoRep1.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) : 208',bty='n')
dev.off()