# R script for Peak Model
#  -- generated by MACS
p <- c(0.0364482440909,0.0427500060747,0.0489561661068,0.0556164354095,0.0622209369071,0.0624599417864,0.0627706481294,0.0626591125191,0.0632088237415,0.0633362930104,0.0636469993535,0.0632088237415,0.0635115632552,0.0633044256932,0.0632725583759,0.0637027671587,0.0636549661828,0.0636788666707,0.0632406910587,0.0638461700862,0.0638780374035,0.0645631847241,0.0646269193586,0.0646348861879,0.064587085212,0.0644038481379,0.0642604452103,0.0642763788689,0.0642445115517,0.0639338052086,0.0638222695983,0.0636708998414,0.0634876627673,0.0636549661828,0.0633601934984,0.0632167905708,0.063479695938,0.0635991983776,0.0637904022811,0.0640851749655,0.064356047162,0.0639816061845,0.0645233505775,0.0643480803327,0.0647942227741,0.0645791183827,0.0645392842362,0.0642206110638,0.0644755496017,0.0647942227741,0.0647065876517,0.0651367964344,0.0646428530172,0.0641648432586,0.0641489096,0.0644436822844,0.0645711515534,0.0648021896034,0.0645631847241,0.0643719808207,0.0642684120396,0.064252478381,0.06437994765,0.0651925642395,0.0650172939947,0.0652483320447,0.0654793700947,0.0658617779015,0.0658777115601,0.0658458442429,0.0660928159515,0.0660689154636,0.0657821096084,0.0657263418033,0.0655192042412,0.0654554696067,0.0657263418033,0.0653359671671,0.0652005310688,0.0646508198465,0.0646428530172,0.0645153837482,0.064483516431,0.0643879144793,0.0642923125276,0.0644197817965,0.0639816061845,0.0637266676466,0.0639975398431,0.0643082461862,0.0641568764293,0.0646508198465,0.0650889954585,0.0653758013137,0.0654714032654,0.0656785408274,0.0654634364361,0.0659733135119,0.0661406169274,0.0663158871722,0.0665469252221,0.0669452666876,0.067136470591,0.066594726198,0.0669054325411,0.0663158871722,0.0662202852205,0.0663955554653,0.0662362188791,0.0659175457067,0.066052981805,0.0654634364361,0.0652403652154,0.0657980432671,0.0653758013137,0.066363688148,0.0674312432755,0.0672081720548,0.0670886696152,0.067160371079,0.0668655983945,0.0670807027859,0.0670727359566,0.0668576315652,0.0676782149841,0.0674551437634,0.0665309915635,0.0665867593687,0.0665708257101,0.066722195467,0.0667540627842,0.0667460959549,0.0669054325411,0.067056802298,0.06680186376,0.0669133993704,0.0670249349807,0.0674232764462,0.0675029447393,0.0678614520582,0.0680128218151,0.0681801252306,0.0683394618168,0.0684111632806,0.0687457701116,0.0685704998668,0.0691202110891,0.0686979691357,0.0692317466994,0.0697814579218,0.0700284296304,0.0703152354855,0.0703072686562,0.0709924159768,0.0710720842699,0.0716775632975,0.0717253642733,0.0725300140336,0.0734143320869,0.0737409720886,0.0740676120903,0.0738445408696,0.0737409720886,0.0731753272076,0.0733027964766,0.0727371515956,0.0727291847663,0.0731036257439,0.0725220472043,0.0722511750077,0.0719803028112,0.0724822130577,0.0731992276956,0.0736374033076,0.0732310950128,0.0734541662335,0.0738365740403,0.0733266969645,0.0737170716007,0.0737728394058,0.0742030481886,0.0743066169696,0.0743225506282,0.0740915125782,0.0748403945333,0.0753662052677,0.0753901057557,0.0755335086832,0.0755335086832,0.0756131769763,0.0757884472212,0.0758043808798,0.0755175750246,0.0757087789281,0.0756450442936,0.0757247125867,0.0762027223452,0.0763461252728,0.0759557506366,0.0758601486849,0.075732679416,0.0753662052677,0.0755096081953,0.0757087789281,0.0758760823436,0.0758043808798,0.0753184042919,0.0755096081953,0.0762106891746,0.0764895282004,0.0771029740572,0.0774614813761,0.078409534064,0.0785768374795,0.0783457994295,0.0787680413829,0.0792141838242,0.0794213213863,0.0795965916311,0.0797957623638,0.0796125252897,0.080082568219,0.0798435633397,0.0799232316328,0.0805605779775,0.080520743831,0.0803693740741,0.0803614072448,0.0804729428551,0.0804809096844,0.0804570091965,0.0804251418793,0.0806322794413,0.0808155165154,0.080751781881,0.0804092082207,0.0806880472465,0.0807199145637,0.0806322794413,0.0809350189551,0.0811023223706,0.0811580901757,0.0808792511499,0.0809111184672,0.0812058911516,0.0817078013981,0.0822176784739,0.0829824940876,0.0830541955514,0.0837632433599,0.0839863145806,0.0845280589737,0.0852530404408,0.0857788511752,0.0855876472718,0.0858983536149,0.0858585194683,0.085746983858,0.0860098892252,0.0855637467839,0.0862727945924,0.0858585194683,0.086312628739,0.0865755341062,0.0872447477682,0.0876908902095,0.0878661604543,0.0882645019198,0.0888859146059,0.0889098150939,0.0889576160697,0.0896905643662,0.0895471614386,0.0895869955852,0.0898977019283,0.0897941331472,0.0900729721731,0.0898499009524,0.0898100668058,0.0899534697334,0.0900411048558,0.0905908160782,0.0904155458334,0.0904394463213,0.0903438443696,0.0907979536402,0.0906943848592,0.0912918970574,0.091331731204,0.0919212765729,0.092208082428,0.0919451770608,0.0918256746211,0.0924072531607,0.0931242677986,0.0932995380434,0.0943989604881,0.0946379653674,0.0954824492742,0.0962074307414,0.0969563126965,0.0976255263585,0.0987329156325,0.0994578970996,0.100214745884,0.10117873223,0.102310021992,0.103680316634,0.104803639566,0.10567999079,0.106046464939,0.107042318602,0.108093940071,0.108619750806,0.109113694223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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('Cavia_porcellus-male-liver-H3K4me3-ERR572201.50mers.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()