# R script for Peak Model
#  -- generated by MACS
p <- c(0.0270782138748,0.0316693297221,0.03646865944,0.0410077218196,0.0455363735057,0.0456821232151,0.0455155521186,0.045463498651,0.0457862301505,0.0463171755205,0.0463171755205,0.045973622634,0.0458695156987,0.0459319798599,0.0459111584728,0.0460673188758,0.0466294963265,0.0469314064389,0.0469626385195,0.0466815497941,0.0467023711812,0.0470563347613,0.0470979775354,0.0470875668419,0.0472749593254,0.0471916737772,0.0468272995036,0.0469001743583,0.046973049213,0.0468897636648,0.0469001743583,0.0473686555672,0.0473374234866,0.0474519411155,0.0472957807125,0.0471083882289,0.0470042812936,0.0468481208906,0.0465982642459,0.0467544246489,0.0471916737772,0.0468585315842,0.0473686555672,0.0473270127931,0.0476289229055,0.0481182255015,0.048617938791,0.048461778388,0.0486283494845,0.0483680821462,0.0485867067104,0.0488782061292,0.0483680821462,0.0487324564198,0.048951080984,0.0486699922586,0.0489198489034,0.0491905269352,0.0497422936923,0.0504085780783,0.050127489353,0.0502524176754,0.0507104881907,0.0508562379002,0.0510644517708,0.0514496474315,0.0512310228673,0.0512206121738,0.050814595126,0.050970755529,0.0510228089967,0.0506584347231,0.0503981673848,0.0507521309649,0.0506688454166,0.0504710422395,0.0506792561101,0.0508562379002,0.0511997907867,0.0513351298026,0.0512310228673,0.0513975939638,0.0519910034951,0.0520222355757,0.052126342511,0.0521992173657,0.0525219488652,0.0528446803646,0.0527301627358,0.0522408601398,0.0528550910582,0.0531153583965,0.0526260558005,0.0524698953975,0.0523449670751,0.0519910034951,0.051814021705,0.0521783959786,0.0525427702522,0.0521992173657,0.051970182108,0.0520846997369,0.0525948237199,0.0523345563816,0.0525115381716,0.0530841263159,0.0531570011706,0.0528550910582,0.0533339829606,0.0540731422013,0.054146017056,0.0540314994272,0.0537087679277,0.0540627315078,0.0542917667655,0.0544166950879,0.0544062843943,0.0544375164749,0.0544999806361,0.0544895699426,0.0545208020232,0.055124622248,0.0551974971027,0.0552599612639,0.055280782651,0.0555098179086,0.0557804959405,0.0558429601016,0.055124622248,0.054968461845,0.0547602479744,0.0544687485555,0.054791480055,0.0546769624261,0.0549059976838,0.0548747656032,0.0552079077962,0.0554473537475,0.0558637814887,0.0564051375523,0.0577168849373,0.0576752421631,0.0581749554526,0.0590078109351,0.0593305424346,0.0597365594823,0.0593825959023,0.0591639713381,0.0591639713381,0.059143149951,0.0581333126785,0.0589245253869,0.0585289190327,0.0584456334845,0.0584144014039,0.0587579542904,0.0591743820316,0.0594242386764,0.0594450600635,0.0598198450306,0.0604965401101,0.0602258620783,0.0604236652554,0.0603924331748,0.05978861295,0.0596012204664,0.0599135412724,0.0604653080295,0.0607776288355,0.0605173614972,0.0602466834654,0.0604861294166,0.0611003603349,0.0616729484791,0.0623704649457,0.062453750494,0.0627244285258,0.0628909996223,0.0630263386382,0.0633698915247,0.0638071406531,0.0643589074102,0.0642027470072,0.0640153545237,0.0645671212808,0.0644421929585,0.0647336923773,0.064962727635,0.0650356024897,0.0650460131833,0.0651917628927,0.0648377993126,0.0652021735862,0.0655353157792,0.0657331189563,0.0669199380189,0.0667117241483,0.0668991166318,0.0669824021801,0.0673884192278,0.0677736148885,0.0683774351133,0.0687522200804,0.0688875590963,0.0690437194993,0.0690437194993,0.0691374157411,0.0688355056286,0.0694809686276,0.06978287874,0.0699910926106,0.0698453429012,0.0700535567718,0.0702097171748,0.0701680744006,0.0702825920295,0.0705220379807,0.0711883223667,0.0721565168651,0.0725937659934,0.0726978729287,0.0734162107824,0.0732288182988,0.0738326385236,0.0739263347654,0.0737285315883,0.0739679775396,0.0743115304261,0.0735203177177,0.0737389422819,0.0737389422819,0.0740824951684,0.0748737078768,0.0749465827315,0.075269314231,0.0763103835841,0.07662270439,0.0767684540995,0.0779240410814,0.0779656838556,0.0790483959828,0.0791837349987,0.0791733243052,0.0799437156265,0.0800790546424,0.0800061797877,0.0803080899001,0.080620410706,0.0801935722712,0.0808286245766,0.0808078031896,0.081619837285,0.0816927121397,0.0818384618492,0.0826504959446,0.08328554825,0.0833688337983,0.0834000658789,0.0839414219425,0.0834625300401,0.0836499225236,0.0830148702182,0.0838997791684,0.0836082797495,0.0836707439107,0.083951832636,0.084774277425,0.0855654901334,0.0855134366657,0.0869397016795,0.0873040759531,0.0878350213232,0.0874602363561,0.0878870747908,0.0883243239192,0.0881889849032,0.088928144144,0.0896048392235,0.0906354978831,0.090281534303,0.0902398915289,0.0903127663836,0.0916557458492,0.0928842076858,0.0933526888947,0.0938836342648,0.0936441883136,0.0935192599912,0.0932173498788,0.0942271871514,0.0946956683603,0.095257845811,0.0946852576667,0.0947477218279,0.0952890778916,0.0960907012935,0.0965487718088,0.0965591825024,0.0973712165978,0.0971838241142,0.0980895544515,0.0989952847887,0.100192514545,0.100234157319,0.101316869446,0.10224342117,0.103700918265,0.105262522295,0.106720019389,0.108364908967,0.109541317336,0.111050867898,0.110728136398,0.11167550951,0.111290313849,0.1112070283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m <- 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ycorr <- 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altd  <- c(249)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('Macaca_mulatta-male-liver-H3K4me3-ERR572234.50mers.unique.MACS2_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) : 249',bty='n')
dev.off()