# R script for Peak Model
#  -- generated by MACS
p <- c(0.0216653245066,0.0247783392035,0.0284259119797,0.0316647050481,0.0351864994527,0.0355009453817,0.0360355034609,0.0353122778243,0.0346519413734,0.0345576075947,0.0355009453817,0.0359726142752,0.0367272845047,0.0375762885129,0.0377020668845,0.0376391776987,0.0375133993271,0.0380165128135,0.0377335114774,0.0382680695567,0.0382051803709,0.0382995141496,0.0377649560703,0.0374505101414,0.0370731750266,0.0373247317698,0.0366958399118,0.0360983926467,0.0362241710183,0.0358468359036,0.0362556156112,0.0362556156112,0.0357525021249,0.0359411696823,0.0364442831686,0.0361927264254,0.0367587290976,0.0371360642124,0.0377964006632,0.0377335114774,0.0377964006632,0.0375762885129,0.0380165128135,0.0377020668845,0.0374819547343,0.0377335114774,0.0374190655485,0.03754484392,0.0375133993271,0.0375133993271,0.0373876209556,0.03754484392,0.0375762885129,0.0373561763627,0.0377964006632,0.0378278452561,0.0378907344419,0.0370102858408,0.0367272845047,0.0373876209556,0.0370731750266,0.0375133993271,0.0372303979911,0.0378907344419,0.0373247317698,0.0371675088053,0.0377335114774,0.0382995141496,0.0385196262999,0.0383938479283,0.0382051803709,0.0378278452561,0.037859289849,0.0374190655485,0.0379221790348,0.0383938479283,0.0377964006632,0.0383938479283,0.0393057411223,0.0392742965294,0.0391485181578,0.0398402992016,0.0403119680951,0.0404377464666,0.0402490789093,0.0399031883874,0.0396201870513,0.0394629640868,0.0387711830431,0.0386768492644,0.0389284060076,0.0391170735649,0.039400074901,0.0394315194939,0.0403748572809,0.0406578586169,0.042167199076,0.0426388679695,0.0432048706417,0.0439280962783,0.0448085448795,0.0444312097647,0.0440538746499,0.0444940989505,0.0438652070925,0.0438337624996,0.0439280962783,0.0435193165706,0.0435822057564,0.0432992044204,0.0430790922701,0.0432363152346,0.0426388679695,0.0421986436689,0.0425759787837,0.0431734260488,0.0418213085542,0.0419156423328,0.0416011964039,0.0411295275104,0.0410980829175,0.040343412688,0.0411609721033,0.0419785315186,0.0421043098902,0.0416011964039,0.0424187558192,0.0432048706417,0.0433306490133,0.0443683205789,0.0448714340652,0.0458462164451,0.0463493299314,0.0465694420817,0.0463493299314,0.046789554232,0.0475442244616,0.047104000161,0.04741844609,0.0469467771965,0.0466952204533,0.0462235515599,0.0460663285954,0.0454374367374,0.0455946597019,0.0455317705161,0.0447142111008,0.045563215109,0.0452173245871,0.0455317705161,0.0461292177812,0.0461606623741,0.0466008866746,0.0473241123113,0.0480473379479,0.0483617838769,0.0488648973633,0.048015893355,0.0477957812047,0.0475756690545,0.0469467771965,0.0472926677184,0.0475127798687,0.0477643366119,0.047104000161,0.046789554232,0.0468838880107,0.0477014474261,0.0479530041692,0.0477014474261,0.0479530041692,0.0487076743988,0.0488648973633,0.0490535649207,0.0496510121857,0.0505314607869,0.0509087959016,0.0499340135218,0.0510345742732,0.0513804647951,0.051726355317,0.051726355317,0.0515691323525,0.0507515729371,0.0510660188661,0.0509402404945,0.0511289080519,0.0514433539809,0.0510031296803,0.0512861310164,0.0511917972377,0.051097463459,0.0512861310164,0.0525439147323,0.0525753593252,0.0528583606613,0.052040801246,0.0524495809536,0.0523866917678,0.0531413619974,0.0542733673417,0.0543362565275,0.0539274768198,0.0524181363607,0.05295269444,0.052638248511,0.0543048119346,0.0550280375713,0.0557827078008,0.0555311510576,0.054807925421,0.0556254848363,0.0559713753582,0.0570719361096,0.0569776023309,0.0576064941889,0.0576064941889,0.0574807158173,0.0573234928528,0.0582039414539,0.0587384995332,0.058172496861,0.0586127211616,0.059713281913,0.0607823980716,0.0609081764432,0.0608767318503,0.0615370683011,0.0627005182383,0.0628891857957,0.0621345155662,0.0629520749815,0.0642413032903,0.0638010789898,0.0632036317247,0.0640840803258,0.0646186384051,0.0651531964844,0.0648387505554,0.0653418640418,0.0661594234571,0.0665996477577,0.0666625369435,0.0677002085091,0.0673543179872,0.0673543179872,0.0669769828724,0.0669455382795,0.0685806571102,0.0683919895528,0.0690837705966,0.0698384408262,0.0699013300119,0.0703101097196,0.071127669135,0.0715050042497,0.0722282298864,0.0732030122662,0.0723854528509,0.0730457893017,0.0731086784875,0.0735489027881,0.0730457893017,0.0722282298864,0.072668454187,0.073580347381,0.0735489027881,0.0737061257526,0.0741149054603,0.0738319041242,0.0753412445833,0.0753412445833,0.0762531377773,0.078800149802,0.0794919308458,0.078517148466,0.079743487589,0.0790202619523,0.0796491538103,0.0800893781109,0.0806868253759,0.0830766144361,0.0832338374006,0.0827307239143,0.0832652819935,0.0845230657095,0.0847431778597,0.0860638507614,0.0867241872123,0.0886108627862,0.088044860114,0.0869128547697,0.0882964168572,0.0879819709282,0.0878561925566,0.0873216344774,0.0872587452916,0.0875731912205,0.0870071885484,0.085592181868,0.0865355196549,0.0869442993626,0.0877618587779,0.0882649722643,0.0910320964393,0.0931703287564,0.093893554393,0.0949312259586,0.0960946758959,0.0989246892567,0.0999623608223,0.100622697273,0.100685586459,0.101754702617,0.1004340297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m <- 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ycorr <- 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altd  <- c(231)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('A549-100nM-Dex-0.5h-p300.pooled.sorted.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) : 231',bty='n')
dev.off()