# R script for Peak Model
#  -- generated by MACS
p <- c(0.0424185653568,0.0494379436884,0.0565665212275,0.0637117449874,0.0707664133067,0.070703823517,0.0706498897621,0.0706359069367,0.0708190153641,0.0707650816091,0.0708023691434,0.0709355389087,0.0709581777689,0.0708942562815,0.0709342072111,0.0709668338036,0.0709828141754,0.070992136059,0.0707744034927,0.0708150202711,0.070773071795,0.0706798529593,0.0705853024259,0.0705786439376,0.0704767690671,0.0704434766258,0.0703995306032,0.0703189628952,0.0703376066623,0.0703242896858,0.0703489260924,0.0703682357084,0.0703256213834,0.0702663608379,0.0702610340472,0.0703356091158,0.0703376066623,0.0703702332548,0.0703402700576,0.0702210831176,0.0701884565251,0.0701205399448,0.0700406380856,0.070085249957,0.0702177538735,0.0701864589787,0.0702636974426,0.0702816753609,0.0703555845806,0.0704408132305,0.0704547960558,0.0705833048794,0.0707224672842,0.0707431085978,0.0706598774945,0.070688508994,0.0705932926118,0.0703882111732,0.0703649064642,0.0703129702557,0.0702823412097,0.0701644859674,0.0700479624227,0.0699793799935,0.0698881587043,0.0697383427183,0.0697230281952,0.0699653971682,0.0700479624227,0.0701172107007,0.0700959035382,0.0700752622246,0.0701172107007,0.0700859158058,0.0700719329805,0.0702344000942,0.0702437219778,0.0701651518162,0.070139183712,0.0700646086434,0.0701178765495,0.0702756827214,0.0701731420021,0.0703123044069,0.0703635747666,0.0701511689908,0.0701418471073,0.0700066797954,0.069885495309,0.0699993554583,0.0698382200423,0.0696171582318,0.0697256915905,0.0697742985549,0.0699114634132,0.0700013530048,0.0700679378875,0.0701618225721,0.0702810095121,0.0703009849769,0.0703495919412,0.070400196452,0.0703815526849,0.070181132188,0.0700865816546,0.070215756327,0.0701212057936,0.0700752622246,0.0701038937241,0.070081254864,0.0702104295364,0.0702530438613,0.0702144246294,0.0702264099083,0.0702124270829,0.0701564957814,0.070265694989,0.0703962013591,0.0703635747666,0.0702810095121,0.0702936606398,0.0703649064642,0.0705333662174,0.07058863167,0.0706086071348,0.0705446856474,0.070500073776,0.0705113932061,0.0704261645563,0.0703855477778,0.070384881929,0.0702130929317,0.0701897882228,0.070239061036,0.0702057685946,0.070254375559,0.0702956581862,0.070204436897,0.0704181743704,0.0705060664155,0.0705460173451,0.0706485580644,0.070569322054,0.070592626763,0.0706625408898,0.0706971650288,0.0706745261687,0.0708356615847,0.0707997057481,0.0708190153641,0.0706945016335,0.0707710742485,0.0708822710026,0.0708396566777,0.0708982513744,0.0710041213379,0.0709621728618,0.0710007920938,0.0711033328131,0.0712251831484,0.0713836551691,0.0714129525175,0.0716366777233,0.0716386752698,0.0716713018623,0.071668638467,0.0717458769309,0.0716772945017,0.0716047169796,0.0716413386651,0.0717658523957,0.0716719677111,0.0715594392594,0.0715654318988,0.0714968494697,0.0716013877355,0.0716872822341,0.0717152478849,0.0717452110821,0.0716846188388,0.0715361345505,0.0716573190369,0.0716293533862,0.0717844961628,0.0718444225573,0.0718211178483,0.0718597370803,0.0721194181227,0.072295202213,0.0723191727707,0.0724210476412,0.0725768562667,0.0726014926733,0.0725881756967,0.0726680775559,0.0727892620424,0.072967709528,0.0729084489824,0.072963714435,0.0730928891074,0.0730469455384,0.0731075377816,0.0733079582784,0.073425147672,0.0734997227405,0.0733738773123,0.0733732114635,0.0733858625912,0.0733539018475,0.0735037178335,0.0736788360749,0.0737507477482,0.0738166667821,0.0738959027925,0.0740304042555,0.0741828836368,0.0742248321129,0.0742388149382,0.0743446849017,0.0743699871571,0.0745497663403,0.0744945008877,0.0746083610371,0.0748074498363,0.0748793615096,0.0750078703331,0.075123728029,0.0754673060236,0.075423360001,0.0755418810922,0.0757203285778,0.076045928654,0.0759853364108,0.0760599114794,0.0761990738842,0.0763195925218,0.0765153520769,0.0764121455087,0.0766851435277,0.0768143182001,0.0768968834546,0.0769614707908,0.0771785375083,0.0771958495778,0.0774462087367,0.0775274422935,0.0775434226654,0.0777664820223,0.0779009834854,0.0779735610075,0.0779076419736,0.0780301581577,0.0781287037841,0.0782838465607,0.0782072739457,0.0783570899317,0.0785928004163,0.0787073264145,0.0787233067864,0.0787838990296,0.0790429142232,0.0790868602458,0.0792313494412,0.0793711776948,0.0795822517729,0.0796947802246,0.0797220800265,0.0799484686276,0.0802694077621,0.0804478552477,0.0805111108862,0.0807381653361,0.0809432467748,0.0812209057355,0.0813580705938,0.0813201172107,0.0816537074729,0.0817875430871,0.0819040666318,0.0820019464093,0.0824014557053,0.0825000013317,0.0826365003412,0.08275635313,0.0828435793263,0.0831698452514,0.0832277740993,0.0834248653521,0.0835400571991,0.083767111649,0.0837970748462,0.0841826013169,0.0843690389884,0.0844755748007,0.0846773269952,0.0848611012713,0.0850455413964,0.0851667258828,0.0856175055385,0.0860589633107,0.0864791139203,0.0866875246031,0.0871323116194,0.0878274577945,0.0885012968072,0.089155160355,0.0898136848447,0.0904455753813,0.0909096720135,0.0914556680515,0.0918112313249,0.0922779913525,0.0927267734617,0.0930636929681,0.09324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m <- 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ycorr <- 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altd  <- c(251)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('A549-100nM-Dex-12h-H3K27ac.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) : 251',bty='n')
dev.off()