# R script for Peak Model
#  -- generated by MACS
p <- c(0.0432898487567,0.0505481385935,0.0576148758453,0.0648358905845,0.0720537990655,0.0720154885486,0.0721179950669,0.072104534615,0.0721687306164,0.0720807199693,0.0721480222289,0.0721625181002,0.0723778853307,0.0723706373951,0.072384097847,0.0724317271383,0.072540446173,0.0724607188809,0.0722153244884,0.0722774496511,0.0723934166214,0.0721832264877,0.0722173953272,0.0720299844198,0.0720486219686,0.0720931450019,0.0720858970662,0.0722163599078,0.0724917814622,0.0724545063646,0.0722774496511,0.0722836621673,0.0721946161009,0.072354070685,0.072384097847,0.0724079124926,0.0721480222289,0.0719471508696,0.0717079689934,0.0716189229269,0.0715526560868,0.0717121106709,0.0716810480896,0.0716127104107,0.0715215935055,0.0714501495684,0.071495708021,0.0714159807289,0.071424264084,0.0715050267954,0.0714894955047,0.0714118390514,0.071424264084,0.0714429016328,0.0712948366618,0.0711881884659,0.0713165804687,0.0714014848577,0.0712492782092,0.0710111317523,0.0711260633032,0.0711302049807,0.0709873171066,0.0709490065897,0.0709655732997,0.0710132025911,0.0708972356208,0.0708475354907,0.0710763631731,0.0713362534369,0.0712938012424,0.071254455306,0.0713207221462,0.0714501495684,0.0715837186681,0.0715536915062,0.0714801767303,0.0716468792501,0.071470857956,0.0712161447891,0.0711219216257,0.0711560904652,0.0712368531766,0.0712109676922,0.0711540196264,0.0712358177572,0.0713124387912,0.0713082971137,0.0713952723414,0.0715982145394,0.0717421378329,0.0715775061518,0.071457397504,0.0712958720811,0.0711840467884,0.0709873171066,0.0709479711703,0.0707905874249,0.0708496063294,0.0706932580034,0.0705379450968,0.0708112958124,0.0709003418789,0.0709241565246,0.0710132025911,0.0711374529164,0.0710773985925,0.0711426300133,0.0709655732997,0.0709862816872,0.0710856819475,0.0708609959426,0.0706766912934,0.0706663370996,0.0706601245833,0.070683939229,0.0707139663909,0.0708361458775,0.0709345107184,0.0709282982021,0.0709075898146,0.0708527125875,0.0708547834263,0.0709593607834,0.0708692792976,0.0708651376201,0.0710308047205,0.0707574540048,0.0707419227141,0.0708102603931,0.0708423583938,0.0709355461377,0.0710618673018,0.0710308047205,0.0710877527863,0.0711643738202,0.0709138023308,0.0710846465281,0.0711074257544,0.0712451365316,0.0711809405302,0.0712244281441,0.0712099322728,0.0710546193662,0.0709697149772,0.0708351104581,0.0711074257544,0.0711333112389,0.0711881884659,0.0711602321427,0.0712327114991,0.071237888596,0.0711799051109,0.0713890598251,0.0715702582162,0.0715650811193,0.0714263349227,0.0713507493082,0.0713031200168,0.0711032840769,0.0711571258845,0.0710546193662,0.0710453005918,0.0712679157579,0.0713082971137,0.0714377245359,0.0715826832487,0.0716220291851,0.0715557623449,0.0716769064121,0.0716996856384,0.0720403386136,0.0721946161009,0.0720310198392,0.0718311838993,0.0717183231872,0.0716085687332,0.0717555982848,0.0718684589969,0.0716572334439,0.0715920020231,0.0714677516978,0.0714822475691,0.0715226289248,0.0718073692537,0.0719450800309,0.0720279135811,0.0718757069326,0.0719067695139,0.0723364685556,0.0723499290075,0.0723975582989,0.0724897106235,0.0724710730747,0.0723685665563,0.0726491652076,0.072688511144,0.0728593553413,0.0728666032769,0.0727578842423,0.0730591912811,0.0730032786348,0.0729608264403,0.072971180634,0.0729794639891,0.0726709090146,0.0727040424346,0.0727319987578,0.0727930885011,0.0730540141843,0.0728593553413,0.0730260578611,0.0730881830237,0.0732952668992,0.0734712881934,0.0736359198744,0.0737632764579,0.0739517227846,0.0739848562047,0.0738792434282,0.0739817499466,0.0740345563348,0.0741567358214,0.0741867629833,0.0741422399501,0.074218860984,0.0741691608539,0.0739931395597,0.0741246378207,0.0741867629833,0.0743068716311,0.074421803182,0.0745677973143,0.0746299224769,0.0749830004847,0.0749322649352,0.0750182047435,0.0751476321657,0.0752107927477,0.0752812012654,0.0754996747541,0.0754986393347,0.0754996747541,0.0756052875306,0.075592862498,0.0757119357265,0.0758682840525,0.0758838153431,0.0760360219916,0.0761664848332,0.076075367928,0.0762472475447,0.0763021247717,0.0762079016083,0.0761426701875,0.0763756395475,0.0764957481953,0.0767049029096,0.0769834307221,0.0771511686613,0.0773986338925,0.0774773257652,0.0776895867376,0.0780644085523,0.0783315467517,0.0784195573988,0.0785997203705,0.0785924724349,0.0786359600487,0.0785893661767,0.0785479494016,0.0787643520515,0.0788399376661,0.0788761773443,0.078946585862,0.0790905091555,0.0791246779949,0.0795336686491,0.0794342683888,0.0794280558726,0.0795626603916,0.0796278918124,0.0796983003301,0.0797314337502,0.0800441304022,0.0802874539559,0.0804334480882,0.0803889250549,0.0807212946751,0.081039168424,0.0811934459113,0.0813063066235,0.0814906112727,0.0815858698554,0.0813705026249,0.0816076136623,0.081864397668,0.0821760589006,0.0823945323893,0.0828149126566,0.0834817227357,0.0840998681041,0.0846237903092,0.085593978266,0.086710160355,0.0874515206293,0.0881069410953,0.0887789282714,0.0895534219658,0.0904387055336,0.0910672050958,0.0916418628503,0.0920384284719,0.092281752025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m <- 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ycorr <- 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altd  <- c(238)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('Rattus_norvegicus-male-liver-H3K27Ac-ERR572179.50mers.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) : 238',bty='n')
dev.off()