# R script for Peak Model
#  -- generated by MACS
p <- c(0.021951166764,0.0261413525379,0.0296557018967,0.033061917429,0.0369277017237,0.0366844006142,0.0371439693765,0.0374413373992,0.0374413373992,0.0376846385086,0.0377387054218,0.0372250697463,0.0374683708558,0.0377387054218,0.0376035381388,0.0375494712256,0.0370899024633,0.0369817686369,0.0364681329614,0.0364410995047,0.0361437314821,0.0362518653085,0.0359004303726,0.0353327277839,0.0353056943273,0.0351164601311,0.034846125565,0.0345217240857,0.0350623932178,0.0348190921084,0.0347650251952,0.0343595233461,0.0351975605009,0.0361437314821,0.0355219619801,0.0355760288934,0.0353056943273,0.0355489954368,0.0362248318519,0.035873396916,0.0360896645689,0.0362788987651,0.0353056943273,0.0347650251952,0.0352786608707,0.0351705270443,0.0361437314821,0.0353327277839,0.0351975605009,0.0356571292632,0.0357111961764,0.0350894266745,0.0353056943273,0.0352245939575,0.0351975605009,0.0354408616103,0.0354138281537,0.0357922965462,0.0355219619801,0.0358193300028,0.0365221998746,0.0376035381388,0.0381982741841,0.0381982741841,0.0381712407275,0.0387119098596,0.0380631069011,0.0389822444257,0.0388741105993,0.0386308094898,0.0381712407275,0.0383064080106,0.0381982741841,0.0386578429464,0.0386308094898,0.0385226756634,0.0391444451653,0.0386308094898,0.0387389433162,0.039576980471,0.0392255455352,0.0383875083804,0.0380631069011,0.0379009061615,0.0381982741841,0.0379820065313,0.0374413373992,0.0372791366595,0.0379279396181,0.0369277017237,0.0370899024633,0.0374143039426,0.0376035381388,0.0380360734445,0.0382253076407,0.0385767425766,0.03854970912,0.039441813188,0.0387659767729,0.0393877462748,0.0396580808408,0.0399554488635,0.0399284154069,0.0396310473842,0.0391444451653,0.0390633447955,0.0396580808408,0.0394688466446,0.0393607128182,0.0391714786219,0.0398743484937,0.0399554488635,0.0401717165164,0.0405772183654,0.0410367871277,0.040333917256,0.040198749973,0.0399824823201,0.0407664525617,0.0408475529315,0.0407934860183,0.0410097536711,0.0409556867579,0.0407664525617,0.0407394191051,0.0413882220636,0.0418748242825,0.0416315231731,0.0414422889768,0.0416315231731,0.0417666904561,0.041982958109,0.0420910919354,0.0425236272411,0.0430372629166,0.043145396743,0.0429561625468,0.0436860658751,0.0435508985921,0.0434697982223,0.0435238651355,0.0427128614373,0.0430913298298,0.042875062177,0.0426858279807,0.0430642963732,0.0427128614373,0.042875062177,0.0424965937845,0.0425776941543,0.0422262592184,0.0421992257618,0.0420640584788,0.0420910919354,0.0417666904561,0.0420640584788,0.0427398948939,0.0425236272411,0.0425236272411,0.0421721923052,0.0420640584788,0.0424965937845,0.0434427647657,0.043280564026,0.044037500811,0.0438482666148,0.044172668094,0.0439293669846,0.0450377387054,0.0458487424036,0.0463083111659,0.0467678799282,0.0461731438829,0.0465245788187,0.0468760137546,0.0464705119055,0.0456595082074,0.0456595082074,0.0454162070979,0.0454162070979,0.0454432405545,0.0448214710526,0.0444430026601,0.0444970695733,0.0443348688337,0.0448755379658,0.0449836717922,0.0455784078375,0.0456054412941,0.0453621401847,0.0459839096866,0.046984147581,0.0479843854755,0.0485250546076,0.0484439542378,0.0481465862151,0.0490927571963,0.0492549579359,0.0499307943511,0.0497415601548,0.0494441921322,0.0497415601548,0.0490657237397,0.0487142888038,0.0486602218906,0.0494171586756,0.0499037608945,0.0498226605247,0.0494171586756,0.05041739657,0.0510391660719,0.051174333355,0.0526611734683,0.0531748091438,0.0537965786457,0.0538776790155,0.0538236121023,0.0538776790155,0.0542291139514,0.0538506455589,0.0532559095136,0.0531477756872,0.0520123705097,0.0523097385324,0.0526341400117,0.0534992106231,0.0540669132118,0.0545535154307,0.0554456194987,0.0561755228271,0.0570405934384,0.0568783926988,0.0574190618309,0.0580678647895,0.058716667748,0.0584192997253,0.05782456368,0.0582300655291,0.0580137978763,0.0590410692273,0.0592303034235,0.0600142736651,0.0605279093406,0.0607441769934,0.0603386751444,0.0608793442765,0.0610956119293,0.0613659464954,0.0610956119293,0.0605819762538,0.0604468089708,0.0606630766236,0.0613389130388,0.0605819762538,0.0610956119293,0.0607441769934,0.0611496788425,0.0615551806916,0.0624743182162,0.0632312550012,0.0642585263522,0.0657723999221,0.0667726378166,0.0677188087978,0.0675566080581,0.0687190466922,0.0696381842168,0.0697463180432,0.0712331581565,0.071341291983,0.0713953588962,0.0706113886546,0.0701788533489,0.070449187915,0.0709628235905,0.071611626549,0.071611626549,0.0721522956811,0.0715575596358,0.0729362659227,0.0731255001189,0.0732336339454,0.0733147343152,0.0738013365341,0.0746123402323,0.0746664071455,0.0755314777569,0.075315210104,0.0751259759078,0.0736661692511,0.0740716711002,0.0744771729492,0.0745853067757,0.0753692770172,0.0765317156513,0.0768831505872,0.0765587491079,0.0778022881118,0.078748459093,0.0802893661195,0.0813977378404,0.0829656783235,0.0846687860897,0.0855068232444,0.0859123250935,0.0871558640974,0.0891833733428,0.0901295443241,0.0916163844374,0.0921300201129,0.0922922208525,0.0920489197431,0.0932383918337,0.0940493955319,0.09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m <- 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ycorr <- 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altd  <- c(222)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('A549-100nM-Dex-12h-p300.pooled.sorted.pseudoRep2.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) : 222',bty='n')
dev.off()