# R script for Peak Model
#  -- generated by MACS
p <- c(0.0427085477999,0.0498511127174,0.0569284878196,0.0640447134178,0.0712662962933,0.0713657272237,0.0712847338168,0.0712649793273,0.0714552809094,0.071508618031,0.0715652475676,0.0715217876907,0.0716561182192,0.0716060735125,0.0715803926762,0.0714888635415,0.071430917039,0.0716001471657,0.0715211292077,0.0715362743163,0.0713887741281,0.0715257385886,0.0714124795155,0.0715744663293,0.0715138858949,0.0715329819014,0.0716034395806,0.0714269661411,0.0714467206306,0.0714098455836,0.0714631827052,0.0713637517748,0.0713690196386,0.0713854817132,0.0713637517748,0.0712274457973,0.071199789512,0.0712419324229,0.0712116422057,0.0711675238458,0.0711550126691,0.071160939016,0.071276173538,0.0710536062897,0.0710990416156,0.071199131029,0.0711721332267,0.0710601911195,0.0710345102832,0.0710588741536,0.0709805146786,0.0709568092912,0.0708205033137,0.0709620771551,0.0709785392296,0.0709232266591,0.0710200236576,0.0711135282412,0.0711234054859,0.0710641420174,0.0710911398198,0.0711787180565,0.0712228364164,0.0711062849284,0.0710529478067,0.070966686536,0.0709554923252,0.0710068539979,0.0710713853303,0.0710950907177,0.0711168206561,0.0710397781471,0.0710134388278,0.0711313072817,0.0711642314309,0.0712735396061,0.0712643208443,0.0712577360145,0.0713782384004,0.0715059840991,0.0715336403844,0.0716040980636,0.0716199016552,0.0715764417783,0.0714783278138,0.0715046671331,0.0714342094539,0.0713505821151,0.071199789512,0.0711879368183,0.0711523787372,0.0711010170645,0.0711372336286,0.0710595326366,0.0710865304389,0.0711095773433,0.0711095773433,0.0712030819269,0.0713446557682,0.0714559393924,0.071625828002,0.0715909284039,0.0716291204169,0.0717601585306,0.0717338192112,0.0716778481577,0.0717325022453,0.0716554597363,0.0715652475676,0.0712886847147,0.0711174791391,0.071158305084,0.0711029925135,0.0710680929153,0.0712814414019,0.0714454036647,0.0714348679369,0.0714644996712,0.0713762629514,0.0713999683388,0.0715441761121,0.0715803926762,0.0716021226146,0.0715152028609,0.0713867986792,0.0712873677487,0.0713328030745,0.0714625242222,0.0715764417783,0.0717166986537,0.0717410625241,0.0717219665175,0.0717068214089,0.071822714414,0.0718872457463,0.0718372010396,0.0718767100186,0.0717410625241,0.0716686293959,0.0717259174154,0.0717147232047,0.0718411519375,0.0720393553154,0.0720696455326,0.0722336077954,0.0724700031863,0.0724324696563,0.0725786528785,0.0727202267199,0.0727301039647,0.072795952263,0.0727459075562,0.0726096015787,0.0726714989792,0.0725799698445,0.0725562644571,0.0726135524766,0.0726076261298,0.0726273806193,0.0726925704346,0.0727287869987,0.0727768562565,0.072912503751,0.0729816444642,0.0730534191093,0.0730435418646,0.0730896356734,0.0731989438486,0.073223966202,0.0732121135083,0.073261499732,0.073337883758,0.0734149262671,0.0733760757711,0.0733892454307,0.073493285742,0.0735663773532,0.0736374935153,0.0737547034863,0.0737362659628,0.0737395583777,0.0737178284393,0.0737560204523,0.0739371032726,0.074041802067,0.0741036994674,0.0742459317917,0.0743565569329,0.0743078291921,0.0743361439604,0.074235396064,0.0743486551371,0.0742367130299,0.0742920256005,0.0742281527512,0.0742847822877,0.0743585323818,0.0743295591306,0.0744658651081,0.0746008541196,0.0749070487067,0.0749788233519,0.0752277299195,0.0752099508789,0.0753455983735,0.0754562235146,0.0754463462699,0.0755885785942,0.0755675071388,0.0756649626203,0.0756405987499,0.0756458666137,0.0755740919686,0.0755734334856,0.0756103085327,0.0756399402669,0.0758104873595,0.0758065364616,0.0760053983225,0.0760449073015,0.0760416148866,0.0762701084817,0.076377441208,0.076570376722,0.0766651982716,0.0766698076524,0.0767606783041,0.0768475980579,0.0769101539413,0.077078067102,0.0773710920294,0.0773737259614,0.0776002441075,0.0777200880105,0.0777352331191,0.0778866842052,0.0779044632457,0.0780203562508,0.0781816845816,0.0781981466562,0.0782356801862,0.0783324771847,0.078320624491,0.0783759370616,0.0786261605952,0.0787229575937,0.0787032031042,0.0787328348384,0.0787078124851,0.0788842859246,0.0789804244401,0.0791647996754,0.0792899114421,0.0794222665217,0.0795480367715,0.0796659052255,0.0799470774593,0.0801149906199,0.0802848792296,0.080463986601,0.0805700023613,0.0806088528573,0.0807326476581,0.0807912526436,0.0809427037297,0.0811850254675,0.08124297197,0.0815201933058,0.0817592226287,0.0819126491638,0.0820660756988,0.082174725391,0.082447995829,0.0827739449056,0.0828793021829,0.0829484428962,0.0831367690293,0.0831525726209,0.0832460772045,0.0833178518497,0.0835733432471,0.0839480200645,0.0840079420159,0.0840402076821,0.0841508328233,0.0842970160455,0.0844431992678,0.08455184896,0.0847289808824,0.0850733674826,0.0852142828409,0.0851583117874,0.0853565151653,0.0855593279241,0.0857443616423,0.0859366386734,0.0861789604112,0.0865812935138,0.0868269076665,0.0869777002696,0.0872601894694,0.0876585716742,0.0880213957978,0.0885113071373,0.0891164529987,0.0897202818942,0.0903734970134,0.0910188103368,0.0915818132874,0.092220541781,0.0927367924397,0.0931977305279,0.0937218829824,0.0941433120916,0.094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m <- 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ycorr <- 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altd  <- c(259)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('A549-100nM-Dex-4h-H3K27ac.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) : 259',bty='n')
dev.off()