# R script for Peak Model
#  -- generated by MACS
p <- c(0.0251139990421,0.0292594187558,0.0333243448828,0.0368258159031,0.0402467933367,0.0398443254034,0.0391198831233,0.0385966748099,0.0384759344299,0.03895889595,0.0390393895366,0.0384759344299,0.0385161812233,0.0389991427433,0.0397638318167,0.03968333823,0.0403272869234,0.0406090144768,0.0408102484435,0.0408504952368,0.0407297548568,0.0411322227901,0.0411724695835,0.0409712356168,0.0417359246902,0.0417359246902,0.0419774054502,0.0421786394169,0.0421786394169,0.0416554311035,0.0417761714835,0.0420578990369,0.0419371586569,0.0418566650702,0.0405687676834,0.0401260529567,0.03968333823,0.0400053125767,0.0414541971368,0.0418566650702,0.0416554311035,0.0415749375169,0.0414139503435,0.0412529631702,0.0419371586569,0.0424201201769,0.0426213541436,0.0422993797969,0.0415346907235,0.0414944439302,0.0422188862102,0.0415749375169,0.0417761714835,0.0425811073503,0.0424603669703,0.0417761714835,0.0407297548568,0.0415749375169,0.0412529631702,0.0414944439302,0.0414541971368,0.0422993797969,0.0423798733836,0.0427018477303,0.0422188862102,0.0420981458302,0.0441507322904,0.042782341317,0.043506783597,0.0433457964237,0.0435470303904,0.043627523977,0.0438287579437,0.0435470303904,0.043627523977,0.0441909790837,0.0435872771837,0.0437885111504,0.043265302837,0.0439092515304,0.0428628349036,0.0428628349036,0.0429835752836,0.042903081697,0.0438287579437,0.0442714726704,0.0437080175637,0.0439897451171,0.0444324598438,0.043265302837,0.043023822077,0.0428225881103,0.0424603669703,0.043023822077,0.0425006137636,0.0417761714835,0.0423798733836,0.0424201201769,0.0422188862102,0.0420981458302,0.0430640688703,0.0431043156636,0.0436677707704,0.0441104854971,0.0446336938104,0.0450361617438,0.0443519662571,0.0445532002238,0.0449959149505,0.0457606040239,0.0464045527173,0.0469277610306,0.0461630719572,0.0461228251639,0.0457203572305,0.0459618379906,0.0464447995106,0.0459215911972,0.0458008508172,0.0451971489172,0.0453581360905,0.0462838123373,0.046968007824,0.0457606040239,0.0460423315772,0.0462033187506,0.0458813444039,0.0473704757573,0.0469277610306,0.047813190484,0.0477326968974,0.0460423315772,0.0461630719572,0.0467667738573,0.0465252930973,0.0466057866839,0.0472497353773,0.0460020847839,0.0462838123373,0.0460423315772,0.0461630719572,0.046726527064,0.0470082546173,0.0468875142373,0.046847267444,0.047450969344,0.047692450104,0.0480949180374,0.0481351648307,0.0484571391774,0.0482559052108,0.0486583731441,0.0480949180374,0.0484571391774,0.0495438025975,0.0488193603175,0.0492218282508,0.0486181263508,0.0491413346642,0.0492218282508,0.0503487384643,0.0501475044976,0.0499462705309,0.0500670109109,0.0488596071108,0.0491413346642,0.0480144244507,0.0496242961842,0.0499462705309,0.0512341679177,0.0507109596043,0.0504292320509,0.0510731807443,0.051395155091,0.0521195973711,0.0520793505777,0.0532465075845,0.0527232992711,0.0515963890577,0.0507109596043,0.0505902192243,0.0514354018844,0.0519586101977,0.0518781166111,0.0513146615043,0.0520391037844,0.0523610781311,0.0531660139978,0.0541319370379,0.0536892223112,0.0534879883445,0.0540111966579,0.0535684819312,0.0543331710046,0.0551381068713,0.0558223023581,0.0543331710046,0.0540514434512,0.0541721838313,0.0543734177979,0.054856379318,0.0550576132847,0.0561442767048,0.055218600458,0.0562650170848,0.0556613151847,0.0555003280114,0.055339340838,0.055218600458,0.055097860078,0.054977119698,0.0536087287245,0.0531660139978,0.0541319370379,0.0538099626912,0.0541721838313,0.054735638938,0.0556613151847,0.0552990940447,0.0558223023581,0.0560637831181,0.0585993310983,0.058559084305,0.0584383439249,0.0577139016449,0.0576334080582,0.0588810586517,0.0590822926183,0.0594847605517,0.0606116707651,0.0606921643518,0.0592030329983,0.0600079688651,0.0602896964184,0.0616178405986,0.0622617892919,0.0614166066319,0.0611348790785,0.0630667251587,0.0622617892919,0.0629057379853,0.0635496866787,0.0635496866787,0.0642338821654,0.0649180776522,0.0651193116188,0.0663267154189,0.0666486897656,0.0649180776522,0.0652400519989,0.0654412859655,0.0659644942789,0.0663267154189,0.0665279493856,0.0660449878656,0.0667291833523,0.0670914044923,0.0668499237323,0.0674938724257,0.0678560935657,0.0674938724257,0.0673731320457,0.0676548595991,0.066930417319,0.0669706641123,0.0669706641123,0.067051157699,0.0678560935657,0.0691842377459,0.0700696671993,0.0703513947526,0.0703513947526,0.0701099139926,0.0704721351326,0.0708343562727,0.0707941094793,0.0710355902393,0.0711965774127,0.0707136158927,0.0707941094793,0.0716392921394,0.0720820068661,0.0728466959395,0.0729271895262,0.0740943465329,0.0746578016397,0.074577308053,0.0755432310931,0.0765896477198,0.0771531028265,0.0779177918999,0.0777165579332,0.0781995194533,0.0793264296667,0.0792056892867,0.0783605066266,0.0806545738468,0.0802521059135,0.0815400033002,0.0815400033002,0.0814192629202,0.0830291346537,0.0839950576938,0.0856451762206,0.0881002306141,0.0899113363143,0.089991829901,0.0917626888078,0.0919236759811,0.0936945348879,0.0952239130347,0.0971155123216,0.0971960059082,0.0989266180217,0.097517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m <- 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ycorr <- 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altd  <- c(227)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('A549-100nM-Dex-1h-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) : 227',bty='n')
dev.off()