# R script for Peak Model
#  -- generated by MACS
p <- c(0.0476420599986,0.0554864853188,0.0634727024842,0.0712420615333,0.0789572060534,0.0786569409694,0.0790864868535,0.0789488653566,0.0784442532015,0.0782315654337,0.0779646631368,0.0782065433433,0.0779313003497,0.0779646631368,0.0780856032401,0.0780730921949,0.0781481584659,0.0777769974593,0.0776477166592,0.0779688334852,0.0780564108013,0.0779604927884,0.078181521253,0.078331653795,0.078331653795,0.0783566758854,0.0783816979757,0.0784942973822,0.0788112438598,0.0785443415629,0.0786736223629,0.0784567642467,0.0784525938983,0.0782232247369,0.0780272183626,0.0782690985692,0.0780021962723,0.0779062782593,0.0778270416399,0.0775851614334,0.0774141771494,0.077259874259,0.0770054830072,0.077013823704,0.0771806376396,0.0767260696652,0.0769637795234,0.0768053062846,0.0767010475748,0.0767344103619,0.0768011359362,0.0771722969428,0.0770388457944,0.0765300632909,0.0762256278585,0.0765675964264,0.0758252744131,0.0759253627744,0.0760671546197,0.0758836592905,0.0756876529162,0.0752205738967,0.0753123215612,0.075566712813,0.0754249209677,0.075074611703,0.0757251860518,0.075771059884,0.0757502081421,0.075942044168,0.0761463912391,0.0764299749295,0.0762965237811,0.0763257162198,0.0768762022072,0.0771180824138,0.0767302400136,0.0764591673683,0.0761589022842,0.0760754953164,0.0760337918326,0.0756292680388,0.0759003406841,0.0759587255615,0.0754165802709,0.0750912930966,0.0748744349803,0.075095463445,0.075224744245,0.0750370785675,0.0747159617416,0.0746200437286,0.0743072675994,0.0742238606316,0.0740320246057,0.0738109961411,0.0738944031089,0.073702567083,0.0735190717538,0.0733856206054,0.0730478223859,0.0731270590053,0.0728226235728,0.0725724026695,0.0726015951082,0.0727558979986,0.0727517276502,0.0726474689405,0.0726057654566,0.0726558096373,0.0727475573018,0.0727475573018,0.0730144595987,0.0732271473666,0.0733272357279,0.0735899676765,0.0736650339475,0.0735440938442,0.0733689392118,0.0736108194184,0.0733981316506,0.0729894375084,0.0730770148246,0.0732771915473,0.0733647688634,0.0728226235728,0.0728393049664,0.0726182765018,0.0726015951082,0.0723263521145,0.0725432102308,0.0731395700504,0.07285598636,0.0725807433663,0.0722929893274,0.0723722259468,0.0720135759853,0.0720219166821,0.0718842951853,0.0720219166821,0.0720719608628,0.0713421498947,0.0711086103849,0.0707874935589,0.0707207679847,0.0708542191331,0.0710043516751,0.0713212981527,0.0714756010431,0.0714756010431,0.0716007114948,0.0720052352886,0.0724055887339,0.0722804782822,0.0721845602693,0.0719009765788,0.0715840301012,0.0714464086044,0.0713379795463,0.0712670836237,0.0710752475978,0.071066906901,0.0707499604234,0.07099184063,0.0711294621268,0.071066906901,0.0714464086044,0.0711252917784,0.0711294621268,0.0708792412235,0.0704330139458,0.0704872284749,0.0704330139458,0.0703454366296,0.0704496953394,0.0704538656878,0.0703079034941,0.0706415313653,0.0708458784363,0.0709543074945,0.0716549260239,0.0713713423334,0.0714088754689,0.0712212097914,0.0709876702816,0.070895922617,0.0709209447074,0.0709000929654,0.0708709005267,0.0702912221006,0.0704288435974,0.0702703703586,0.0700618529392,0.0703662883716,0.0706248499717,0.0708166859976,0.0705039098684,0.0700993860747,0.06987835761,0.0707416197266,0.0702912221006,0.0707541307718,0.0709793295848,0.0706790645008,0.0707332790298,0.0707708121653,0.0709584778429,0.0714922824367,0.0716173928884,0.0714797713915,0.0717133109013,0.0714839417399,0.0715423266173,0.0718467620498,0.071913487624,0.0721428567854,0.0723680555984,0.072459803263,0.0727308759083,0.0727267055599,0.0726391282437,0.0728643270567,0.0729685857665,0.0726808317276,0.0725598916243,0.072288818979,0.0724180997791,0.0725390398824,0.0726891724244,0.0724764846565,0.0723430335081,0.0722929893274,0.0718717841401,0.0722429451467,0.0720094056369,0.0719551911079,0.0716924591594,0.0715131341786,0.071046055159,0.0713004464108,0.0712295504882,0.0715715190561,0.0717925475207,0.0717591847336,0.0720302573789,0.0724264404759,0.072459803263,0.07285598636,0.0733731095602,0.0730478223859,0.0736108194184,0.0730853555214,0.0732354880634,0.0731062072633,0.0734314944377,0.0735691159345,0.0734731979216,0.0731395700504,0.0726724910308,0.0730353113407,0.0727350462567,0.073006118902,0.0733689392118,0.0737692926572,0.0735983083732,0.0735482641926,0.0738068257927,0.0738818920637,0.0743281193414,0.0741279426187,0.0741029205283,0.0742780751607,0.074378163522,0.074378163522,0.0743614821285,0.0744865925801,0.0746450658189,0.0746325547738,0.0750037157804,0.0752372552902,0.0755833942065,0.0757376970969,0.0754958168903,0.0756084162969,0.0755917349033,0.0757668895356,0.0757877412776,0.0764299749295,0.0760087697422,0.0762756720391,0.0762965237811,0.0761755836778,0.0764299749295,0.0765884481683,0.0766343220006,0.0764174638844,0.0767052179232,0.0764299749295,0.0766218109554,0.077034675446,0.0775184358591,0.0776268649172,0.0779021079109,0.0785651933048,0.0793408781052,0.0799539193184,0.0804627018219,0.0805669605317,0.0808338628286,0.0813092825449,0.0816929545967,0.0821391818744,0.0824144248681,0.082360210339,0.08261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m <- 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ycorr <- 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altd  <- c(288)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('Mus_musculus_domesticus-male-liver-H3K4me3-ERR572176.50mers.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) : 288',bty='n')
dev.off()