# R script for Peak Model
#  -- generated by MACS
p <- c(0.0196442239394,0.0228783339782,0.0253937528972,0.0275498262564,0.0309037181485,0.0317421911215,0.0327004459478,0.0327004459478,0.0337784826274,0.034018046334,0.0335389189209,0.0343773918939,0.0347367374537,0.0354554285735,0.034856519307,0.0344971737472,0.0350960830136,0.0354554285735,0.034018046334,0.0346169556005,0.0350960830136,0.0341378281873,0.0349763011603,0.0352158648669,0.0360543378399,0.0356949922801,0.0353356467202,0.0332993552143,0.0341378281873,0.0329400096544,0.0330597915077,0.0332993552143,0.034018046334,0.0349763011603,0.034856519307,0.0367730289597,0.0370125926662,0.0384499749057,0.038569756759,0.0396477934386,0.0386895386123,0.0404862664116,0.0397675752919,0.0389291023189,0.0401269208517,0.038569756759,0.0374917200794,0.038569756759,0.0392884478787,0.0398873571452,0.0409653938248,0.0409653938248,0.0413247393846,0.0410851756781,0.0407258301182,0.043121467184,0.0455171042497,0.0459962316629,0.0459962316629,0.0452775405432,0.04479841313,0.0440797220103,0.0430016853307,0.043121467184,0.0420434305044,0.0400071389985,0.0397675752919,0.0388093204656,0.0383301930524,0.0397675752919,0.0415643030912,0.0409653938248,0.0424027760642,0.0428819034774,0.0450379768366,0.0445588494234,0.0443192857169,0.0441995038636,0.0444390675701,0.0420434305044,0.0396477934386,0.0410851756781,0.0416840849445,0.0421632123577,0.0418038667978,0.0425225579175,0.0421632123577,0.0416840849445,0.0419236486511,0.0426423397708,0.0433610308905,0.0425225579175,0.0422829942109,0.0425225579175,0.0410851756781,0.0416840849445,0.0401269208517,0.0406060482649,0.0427621216241,0.0449181949833,0.0464753590761,0.0458764498096,0.0452775405432,0.0453973223965,0.0462357953695,0.045636886103,0.0461160135162,0.0457566679563,0.0433610308905,0.0412049575313,0.0409653938248,0.0421632123577,0.0421632123577,0.0426423397708,0.0426423397708,0.0443192857169,0.0464753590761,0.0473138320491,0.0468347046359,0.0471940501958,0.0457566679563,0.0452775405432,0.0449181949833,0.0443192857169,0.0450379768366,0.0455171042497,0.04479841313,0.0443192857169,0.0445588494234,0.0436005945971,0.0445588494234,0.0450379768366,0.0455171042497,0.0463555772228,0.045636886103,0.0440797220103,0.0436005945971,0.0437203764504,0.0438401583037,0.0459962316629,0.0458764498096,0.0452775405432,0.045636886103,0.0451577586899,0.04479841313,0.0462357953695,0.0453973223965,0.0457566679563,0.0468347046359,0.0465951409293,0.0462357953695,0.0469544864892,0.0465951409293,0.0455171042497,0.0458764498096,0.0455171042497,0.0470742683425,0.0467149227826,0.0457566679563,0.0450379768366,0.0457566679563,0.0459962316629,0.0473138320491,0.0494699054083,0.051027069501,0.0513864150609,0.0519853243273,0.0517457606208,0.0533029247135,0.0553392162194,0.056417252899,0.056417252899,0.054740306953,0.0556985617793,0.0549798706596,0.0549798706596,0.0554589980727,0.0566568166056,0.0556985617793,0.0546205250997,0.0545007432464,0.0541413976865,0.056417252899,0.0556985617793,0.0553392162194,0.0556985617793,0.0549798706596,0.0552194343661,0.0553392162194,0.0548600888063,0.0545007432464,0.0560579073392,0.0560579073392,0.0546205250997,0.0549798706596,0.0543809613931,0.054740306953,0.0535424884201,0.0540216158332,0.0541413976865,0.0548600888063,0.0540216158332,0.0521051061806,0.0537820521267,0.05390183398,0.0530633610069,0.0512666332076,0.0529435791536,0.0541413976865,0.0549798706596,0.0554589980727,0.055578779926,0.0571359440188,0.0573755077253,0.0573755077253,0.0591722355247,0.0612085270306,0.0606096177641,0.0607293996174,0.060968963324,0.0602502722043,0.0607293996174,0.0606096177641,0.0619272181503,0.0624063455635,0.06264590927,0.0622865637102,0.0624063455635,0.0621667818569,0.0634843822431,0.0650415463358,0.0652811100424,0.0642030733628,0.0621667818569,0.0615678725904,0.0612085270306,0.0620470000036,0.0614480907371,0.061807436297,0.0627656911233,0.0624063455635,0.0620470000036,0.0634843822431,0.0627656911233,0.065520673749,0.0652811100424,0.0643228552161,0.0662393648687,0.0667184922819,0.0642030733628,0.0637239459496,0.0652811100424,0.067197619695,0.0691141293476,0.0673174015483,0.068036092668,0.0676767471082,0.0665987104286,0.0668382741351,0.0679163108147,0.0698328204674,0.0679163108147,0.065520673749,0.0651613281891,0.0651613281891,0.065520673749,0.0685152200812,0.0705515115871,0.0698328204674,0.070910857147,0.0699526023207,0.0723482393864,0.072587803093,0.0740251853325,0.0741449671858,0.0746240945989,0.0751032220121,0.0733064942127,0.0747438764522,0.0742647490391,0.0755823494252,0.0735460579193,0.0757021312785,0.0755823494252,0.076301040545,0.0765406042515,0.0751032220121,0.076301040545,0.0752230038654,0.0742647490391,0.0715097664134,0.0731867123595,0.0745043127456,0.0736658397726,0.0745043127456,0.0746240945989,0.073426276066,0.0742647490391,0.0759416949851,0.0768999498114,0.0791758050239,0.0790560231706,0.0778582046377,0.0801340598502,0.0808527509699,0.0827692606226,0.0854044613949,0.0861231525146,0.0869616254877,0.0868418436344,0.0851648976883,0.0852846795416,0.0844462065686,0.085045115835,0.0861231525146,0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m <- 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ycorr <- 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altd  <- c(88)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('SKN7_rep1-GSM5884449.2x25mers.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) : 88',bty='n')
dev.off()