# R script for Peak Model
#  -- generated by MACS
p <- c(0.0237939340084,0.0272431775133,0.0311601150527,0.035953978907,0.0399293782008,0.0394616841662,0.0396955311835,0.0398709164465,0.0395786076749,0.0396955311835,0.0396955311835,0.040338610481,0.0409232280242,0.0402801487267,0.0402216869724,0.0407478427613,0.0414493838131,0.0418586160934,0.0423263101279,0.0423263101279,0.0420924631106,0.0423263101279,0.042150924865,0.0426770806538,0.0435540069686,0.0435540069686,0.0430863129341,0.043261698197,0.0429109276711,0.0428524659168,0.0441386245118,0.0441386245118,0.0440217010032,0.043612468723,0.0431447746884,0.0419170778477,0.041975539602,0.041800154339,0.0418586160934,0.0425601571452,0.0415078455674,0.0417416925847,0.0416247690761,0.0413324603045,0.0414493838131,0.0427940041625,0.0427355424082,0.0428524659168,0.0434955452143,0.04343708346,0.0434955452143,0.0436709304773,0.0439047774946,0.0436709304773,0.0439047774946,0.04343708346,0.0435540069686,0.0446063185464,0.0443140097748,0.0438463157402,0.0447817038094,0.0444893950378,0.0444309332834,0.0441970862662,0.043612468723,0.0432032364427,0.0439632392489,0.0433201599514,0.0433786217057,0.0437293922316,0.0426186188995,0.0429109276711,0.0429693894254,0.0443724715291,0.0445478567921,0.0453663213526,0.0443140097748,0.0443724715291,0.045074012581,0.0446063185464,0.0446063185464,0.0440217010032,0.0444893950378,0.0442555480205,0.0441970862662,0.0438463157402,0.0440801627575,0.0443140097748,0.0441386245118,0.044723242055,0.0451909360896,0.0455417066155,0.0458924771415,0.0457755536328,0.0464770946847,0.0468863269649,0.0474709445081,0.0477632532797,0.0474709445081,0.0476463297711,0.0488740266118,0.0500432616982,0.0500432616982,0.0511540350303,0.0514463438019,0.0513294202932,0.050920188013,0.0509786497673,0.0515048055562,0.0519140378364,0.0518555760821,0.0523232701167,0.0527325023969,0.0521478848537,0.0517971143278,0.052206346608,0.0528494259056,0.052557117134,0.0530832729229,0.0526155788883,0.052557117134,0.0511540350303,0.0509786497673,0.0518555760821,0.052557117134,0.052206346608,0.0526155788883,0.0530832729229,0.0530248111685,0.0527325023969,0.0519724995908,0.0524401936253,0.052206346608,0.0515632673105,0.0513878820476,0.0509786497673,0.0508032645044,0.0510371115216,0.0516217290648,0.0526155788883,0.0526740406426,0.0535509669574,0.0537848139747,0.0531417346772,0.0537848139747,0.0544278932722,0.0552463578327,0.0547786637981,0.0541355845006,0.0539017374833,0.0542525080093,0.0549540490611,0.0559478988845,0.0568248251994,0.0558894371302,0.057117133971,0.0559478988845,0.0563571311648,0.0557140518673,0.0562986694105,0.0560648223932,0.0545448167809,0.0543109697636,0.0551294343241,0.055304819587,0.0549540490611,0.0563571311648,0.0575263662512,0.058578677829,0.0589294483549,0.0600986834413,0.0611509950191,0.0612679185277,0.0606248392302,0.0606833009845,0.0605663774759,0.0612094567734,0.0610340715104,0.061326380282,0.0616186890536,0.0605663774759,0.0605079157215,0.0602740687043,0.0599232981783,0.0604494539672,0.0607417627388,0.0608586862475,0.0607417627388,0.0600986834413,0.0600986834413,0.0615602272993,0.0620279213339,0.0628463858943,0.0637233122092,0.0641910062437,0.0650094708042,0.0644833150153,0.0646587002783,0.0655940883474,0.0656525501017,0.0647171620326,0.0638402357178,0.0629048476487,0.0630217711573,0.0633140799289,0.0629048476487,0.064249467998,0.0640156209808,0.064249467998,0.0635479269462,0.0637817739635,0.0647171620326,0.0660033206276,0.066061782382,0.0659448588733,0.0662956293992,0.0653602413301,0.0659448588733,0.0664125529079,0.0668217851881,0.0677571732573,0.0680494820289,0.0676987115029,0.0679910202745,0.0691602553609,0.0693356406239,0.0699202581671,0.070621799219,0.0705633374646,0.071732572551,0.072083343077,0.0725510371115,0.0725510371115,0.0733110399177,0.0727264223745,0.0725510371115,0.072083343077,0.0720248813226,0.0713818020251,0.070621799219,0.0706802609733,0.0710894932535,0.0712064167622,0.0708556462362,0.0720248813226,0.0720248813226,0.0720248813226,0.0722587283399,0.0726094988658,0.0730187311461,0.0731356546547,0.0722587283399,0.073194116409,0.0736033486893,0.0724925753572,0.073194116409,0.0738371957066,0.0741295044782,0.0752402778103,0.0752402778103,0.076292589388,0.077754133246,0.0775787479831,0.0767602834226,0.0783387507892,0.0785141360522,0.0796249093843,0.0802095269275,0.0806187592077,0.0807356827164,0.0809110679793,0.0802679886818,0.0807941444707,0.0832495381521,0.0830156911349,0.0840680027126,0.0843018497299,0.0840095409583,0.0841264644669,0.0851203142904,0.0845356967472,0.0855295465706,0.0860557023595,0.0851787760447,0.0846526202558,0.0855295465706,0.0857633935879,0.0867572434114,0.0879264784978,0.0874587844632,0.0890957135842,0.0886280195496,0.0888034048126,0.0894464841101,0.0910834132311,0.0900895634076,0.0910834132311,0.0903234104249,0.0882772490237,0.0890957135842,0.088160325515,0.0879264784978,0.0886280195496,0.0903234104249,0.0901480251619,0.0909080279681,0.0904987956879,0.0921357248088,0.0951757360335,0.0960526623483,0.0961111241026,0.0980988237495,0.0978649767322,0.0963449711199,0.0971049739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m <- 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ycorr <- 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altd  <- c(128)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('CFKH2_rep2-GSM5884472.2x25mers.Spar+sacCer3.unique.dedup.MACS-2.1.0_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) : 128',bty='n')
dev.off()