# R script for Peak Model
#  -- generated by MACS
p <- c(0.0518202423385,0.0608479967009,0.0692262499749,0.0778282548201,0.0862997379154,0.085961002898,0.0859206033088,0.0858926343624,0.0860107254694,0.0861878621299,0.0863090608976,0.0857931892197,0.0859889718444,0.0857279283448,0.0857496819698,0.0856284832021,0.0854699925059,0.0856906364163,0.0856875287556,0.0858025122018,0.0854544542023,0.0856222678807,0.0856595598092,0.0854699925059,0.0854358082381,0.0853052864882,0.0852959635061,0.0848391373818,0.0847241539355,0.0841740979898,0.0842548971683,0.0842331435433,0.083711056544,0.0839410234366,0.0837980710439,0.0840808681685,0.0837794250797,0.084021822615,0.0837048412226,0.0840497915614,0.0839099468295,0.0833940751516,0.0834966279551,0.0833412449196,0.0833692138659,0.0832635534018,0.0832386921161,0.0829683256344,0.0827166051169,0.082436915653,0.082393408403,0.082489745885,0.0826451289205,0.0824773152422,0.0821012882963,0.081889967368,0.0817345843325,0.0817314766718,0.0816040625827,0.0817035077254,0.0815388017078,0.0809421308515,0.0807898554767,0.0809265925479,0.080957669155,0.0812528969225,0.0814580025293,0.0811907437083,0.0811689900833,0.0806500107447,0.0803609982987,0.0804821970664,0.0800657705313,0.0800036173171,0.0802957374238,0.0798233729959,0.0794411307286,0.0794753149964,0.0793603315501,0.0794349154071,0.0796586669783,0.0798016193709,0.0797922963888,0.0796959589068,0.0791863025503,0.0794504537107,0.0793696545322,0.0790526731398,0.0789283667114,0.0788662134972,0.0788693211579,0.0785026171942,0.0784528946228,0.0781576668554,0.0781483438732,0.0777288096774,0.0773341367672,0.0773465674101,0.0772160456602,0.0767094969645,0.0763738696078,0.0763738696078,0.0763738696078,0.0763241470365,0.0761128261082,0.0756404616803,0.075932581787,0.0758207060015,0.0757057225552,0.0757927370551,0.0757119378766,0.0760258116083,0.0758952898585,0.0756591076446,0.0756249233767,0.0757026148945,0.0753079419843,0.0749629916455,0.0749598839848,0.0748697618242,0.0742855216108,0.0741083849503,0.0742482296822,0.0742979522536,0.0740586623789,0.0739063870041,0.0741052772896,0.07428241395,0.0742979522536,0.0741736458252,0.0745652110746,0.074186076468,0.0739032793434,0.0734060536298,0.0732568859158,0.0735614366653,0.0730051653982,0.0729896270947,0.0725328009703,0.0722655421493,0.0720386829175,0.0721816353101,0.0719081611676,0.0718460079534,0.0720200369532,0.071839792632,0.0721101591138,0.071818039007,0.0721816353101,0.0726695380416,0.0729336892019,0.0725949541845,0.0726819686844,0.0730704262732,0.072986519434,0.0725763082203,0.0727006146487,0.0728000597914,0.0726322461131,0.0721101591138,0.071979637364,0.0716284717037,0.0715383495432,0.0712835213649,0.0712058298472,0.0712773060435,0.0711902915436,0.0712120451686,0.0708702024905,0.0710131548832,0.0710224778653,0.0712089375079,0.0708919561155,0.0709914012582,0.0707738650085,0.0707334654193,0.0702704239735,0.0700031651524,0.0702424550271,0.0698135978491,0.069471755171,0.0697203680278,0.0696923990814,0.0696302458672,0.0697887365634,0.069900612349,0.069922365974,0.0697980595456,0.069826028492,0.0700528877238,0.0700249187774,0.0697918442242,0.0698695357419,0.0695308007245,0.0691672044215,0.0689279145468,0.0691672044215,0.0690460056538,0.0684897343867,0.0685301339759,0.0683747509404,0.0685456722795,0.0686513327436,0.0689931754217,0.0690739746002,0.0693288027784,0.0691143741894,0.0695028317781,0.0698384591348,0.0700218111167,0.0703636537948,0.0702952852592,0.0702735316342,0.0704568836161,0.0708857407941,0.0706153743123,0.0707552190442,0.0707023888122,0.0706744198658,0.0705936206873,0.0701057179559,0.0698975046883,0.0696395688494,0.0693723100283,0.0686948399935,0.0688812996361,0.0689092685825,0.0687601008685,0.0685953948508,0.0681820759764,0.0685021650295,0.0687663161899,0.0690584362966,0.0689962830824,0.0692666495642,0.0689248068861,0.0683778586011,0.0683747509404,0.0684524424582,0.0686326867793,0.0684990573688,0.0681665376729,0.0682815211191,0.0681478917086,0.0685114880117,0.0687476702256,0.0692666495642,0.0692511112606,0.0695276930638,0.0696457841708,0.0697421216528,0.0697638752778,0.0691703120822,0.0691734197429,0.0691423431358,0.0693940636533,0.0694251402604,0.0693163721355,0.069182742725,0.0690584362966,0.0690056060645,0.0690304673502,0.0689838524396,0.0690428979931,0.0690832975823,0.0689652064753,0.0686699787079,0.0687228089399,0.0685363492973,0.0685114880117,0.0687290242614,0.0689434528503,0.069493508796,0.0694406785639,0.0691423431358,0.0690801899216,0.0694562168675,0.0695525543495,0.069922365974,0.0700218111167,0.070115040938,0.070040457081,0.0698477821169,0.0700466724024,0.0704568836161,0.0705283598124,0.0706619892229,0.0709572169904,0.0707738650085,0.0706495585801,0.0705594364195,0.0705998360087,0.0708391258834,0.0708360182227,0.0705718670624,0.0709385710261,0.0707614343657,0.07069306583,0.070500390866,0.0711312459901,0.071336351597,0.0718988381855,0.0721816353101,0.0728932896127,0.0731978403623,0.0731729790766,0.0737634346115,0.0744626582712,0.0753452339128,0.0756342463589,0.075761660448,0.0757367991623,0.0758921821978,0.0757896293944,0.07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m <- 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ycorr <- 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altd  <- c(2, 256)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('Rattus_norvegicus-male-liver-H3K4me3-ERR572272.50mers.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) : 2,256',bty='n')
dev.off()