# R script for Peak Model
#  -- generated by MACS
p <- c(0.0423028858981,0.0492052475328,0.0561833146121,0.0632239209719,0.070146031853,0.0699979125047,0.069925498601,0.0697971284991,0.0693165635021,0.0691914849412,0.0694120181933,0.069398852029,0.0696160937399,0.0696819245614,0.0696160937399,0.0697773792526,0.069882708567,0.0698662508616,0.0697016738079,0.0699452478474,0.0699287901421,0.0700341194565,0.0696588837739,0.0694679743915,0.0693922689468,0.0694778490148,0.0692573157627,0.0694054351111,0.0695798867881,0.0687471268961,0.0688261238819,0.0687372522729,0.0687997915533,0.0691849018591,0.06940214357,0.0693856858647,0.0694186012754,0.0692968142556,0.0696095106578,0.070188821887,0.0702151542156,0.0703303581532,0.0704784775016,0.0700670348672,0.0702645273317,0.0703106089068,0.0704356874676,0.0706924276715,0.0705607660285,0.0703501073997,0.0702052795924,0.0699584140117,0.0700176617511,0.0701690726406,0.0699024578135,0.0698728339438,0.0695963444935,0.0695930529524,0.0693659366182,0.0697181315133,0.0698958747313,0.070231611921,0.0697905454169,0.0698267523687,0.0697115484311,0.0695074728844,0.069925498601,0.0698695424027,0.0698267523687,0.0695535544595,0.0693033973378,0.0692046511055,0.0693231465842,0.0693461873718,0.0696391345275,0.0701591980173,0.0697707961705,0.0698168777455,0.0699551224707,0.0695535544595,0.069751046924,0.0695173475077,0.0698794170259,0.0699649970939,0.0697806707937,0.069662175315,0.0699386647653,0.0696687583971,0.0693758112414,0.0699320816831,0.0696885076436,0.0696885076436,0.0695469713774,0.0693264381253,0.0697181315133,0.0693593535361,0.0690762810036,0.0692803565503,0.0695272221309,0.0692342749752,0.0694153097343,0.0698761254849,0.0696062191167,0.06940214357,0.0689972840178,0.0691717356948,0.0691454033662,0.069007158641,0.0693330212075,0.0694679743915,0.0694548082272,0.0689775347713,0.0691947764823,0.0692803565503,0.0693758112414,0.0693823943236,0.0695601375417,0.0698037115812,0.0694646828505,0.0693363127485,0.0690400740518,0.0694613913094,0.0694548082272,0.0696983822668,0.0695008898023,0.0695140559666,0.0694383505219,0.0697115484311,0.0699024578135,0.070188821887,0.0703896058926,0.070274401955,0.0702809850371,0.070537725241,0.0707088853769,0.0707319261644,0.0707615500341,0.0707220515412,0.0709524594165,0.0710446225666,0.0712750304418,0.0716798899941,0.071893840164,0.0716469745833,0.0716930561584,0.0716568492065,0.071854341671,0.0715482283511,0.0717062223227,0.0716107676315,0.0715383537278,0.0714692313653,0.0712947796883,0.0709853748272,0.0712519896543,0.071327695099,0.0711038703059,0.0712914881472,0.0710544971898,0.0711631180453,0.0712454065721,0.0708734624306,0.070669386884,0.071149951881,0.070843838561,0.0712157827025,0.0714264413313,0.0716601407476,0.0715317706457,0.0714626482831,0.0715844353029,0.0717950939317,0.0723283235859,0.0721308311214,0.0721703296143,0.071897131705,0.0722690758465,0.0721802042375,0.0724303613592,0.0726508946112,0.0727233085149,0.0729339671437,0.0731281680671,0.0732170396762,0.0737403947071,0.0737798932,0.0734935291265,0.0735856922766,0.0736613977213,0.0735988584409,0.073911554843,0.0739576364181,0.0736251907695,0.0737798932,0.0736120246052,0.0738523071037,0.0741880442933,0.0742045019987,0.0740267587807,0.0741057557665,0.0742505835738,0.0743855367579,0.0744645337437,0.0743987029222,0.0743394551828,0.074039924945,0.0737733101179,0.0736581061802,0.0743197059364,0.0742341258684,0.0739675110413,0.0738983886787,0.0742505835738,0.0749747226103,0.0750833434658,0.0754256637376,0.075484911477,0.0760444734597,0.0756725293183,0.0757416516808,0.0760345988365,0.0758766048649,0.0755803661681,0.075047136514,0.0752479205196,0.07561657312,0.0756725293183,0.0755968238735,0.075748234763,0.0760280157544,0.0758963541114,0.0762551320886,0.0768212771535,0.0769430641733,0.077061559652,0.0765941608193,0.0769957288305,0.0771339735556,0.0774828769096,0.0774269207113,0.0773380491023,0.077236011329,0.077236011329,0.077370964513,0.0775816231419,0.0781839751586,0.0781510597479,0.077937109578,0.0780786458442,0.0783946337874,0.0786579570734,0.0788225341272,0.0789278634416,0.0793162652885,0.0790233181328,0.0792603090902,0.0795104662119,0.0796322532317,0.0792701837134,0.0791878951865,0.0788686157022,0.0788850734076,0.0791418136115,0.0791878951865,0.0796487109371,0.0793195568295,0.0791253559061,0.0795236323762,0.0797375825461,0.0801424420983,0.0806559225061,0.0808698726759,0.0806131324721,0.0808040418544,0.0807974587723,0.0811068636334,0.0813471461319,0.0813208138032,0.0817783380127,0.0816697171572,0.082012037429,0.0821634483185,0.0824991855082,0.082581474035,0.0826505963976,0.0826736371851,0.083193700675,0.0833879015985,0.0836874318363,0.0837960526918,0.0838454258079,0.084286492312,0.0842140784083,0.0840363351903,0.0843523231335,0.0844774016943,0.0842700346066,0.0846716026178,0.0847440165214,0.0854780301812,0.0856129833653,0.0862350846285,0.0871468415063,0.0882659654719,0.0888321105368,0.0899281937148,0.091119731584,0.0918010805866,0.092298103289,0.0929597030451,0.0939734976962,0.0945133104325,0.0948424645401,0.0952308663869,0.0958167606983,0.0954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m <- 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ycorr <- 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altd  <- c(4, 291)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('Monodelphis_domestica-male-liver-H3K4me3-ERR572165.50mers.unique.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) : 4,291',bty='n')
dev.off()