# R script for Peak Model
#  -- generated by MACS
p <- c(0.0351357776894,0.0416579879192,0.0469178348787,0.0538608328652,0.0580687104328,0.0572271349193,0.0578583165544,0.055964771649,0.0555439838922,0.0565959532841,0.0565959532841,0.057647922676,0.057647922676,0.0565959532841,0.0589102859463,0.0608038308517,0.0605934369734,0.0601726492166,0.0597518614598,0.0580687104328,0.057647922676,0.055964771649,0.0593310737031,0.0591206798247,0.0612246186085,0.0586998920679,0.0565959532841,0.0572271349193,0.0591206798247,0.0616454063653,0.0633285573923,0.0633285573923,0.0597518614598,0.0582791043112,0.0549128022571,0.0549128022571,0.0580687104328,0.0578583165544,0.0568063471625,0.0557543777706,0.0538608328652,0.0534400451084,0.0551231961355,0.0561751655274,0.0561751655274,0.055964771649,0.0555439838922,0.0563855594058,0.0557543777706,0.0565959532841,0.0568063471625,0.0582791043112,0.0570167410409,0.0582791043112,0.0595414675815,0.0605934369734,0.0582791043112,0.0591206798247,0.0610142247301,0.0616454063653,0.0614350124869,0.0593310737031,0.0612246186085,0.0618558002436,0.0622765880004,0.0639597390274,0.0660636778112,0.0643805267842,0.0641701329058,0.0650117084193,0.0675364349599,0.0696403737437,0.0679572227166,0.0685884043518,0.0660636778112,0.0629077696355,0.0624869818788,0.0622765880004,0.060383043095,0.0565959532841,0.0555439838922,0.0565959532841,0.0563855594058,0.0536504389868,0.0536504389868,0.0553335900139,0.055964771649,0.0565959532841,0.0580687104328,0.0599622553382,0.0580687104328,0.0561751655274,0.0589102859463,0.0597518614598,0.0597518614598,0.0605934369734,0.0610142247301,0.0635389512707,0.0645909206626,0.0654324961761,0.0675364349599,0.0679572227166,0.0641701329058,0.0626973757572,0.0637493451491,0.0641701329058,0.0624869818788,0.0614350124869,0.0595414675815,0.0582791043112,0.0570167410409,0.0570167410409,0.0589102859463,0.0591206798247,0.0586998920679,0.0599622553382,0.0626973757572,0.0612246186085,0.0639597390274,0.0635389512707,0.0639597390274,0.064801314541,0.0654324961761,0.0645909206626,0.0639597390274,0.0639597390274,0.0608038308517,0.0601726492166,0.0574375287977,0.060383043095,0.0608038308517,0.0593310737031,0.0599622553382,0.0616454063653,0.0641701329058,0.0618558002436,0.0635389512707,0.0626973757572,0.0637493451491,0.0612246186085,0.0605934369734,0.0624869818788,0.060383043095,0.0599622553382,0.0591206798247,0.0586998920679,0.060383043095,0.0643805267842,0.0624869818788,0.0637493451491,0.0641701329058,0.0624869818788,0.0629077696355,0.0635389512707,0.0643805267842,0.0654324961761,0.0641701329058,0.0616454063653,0.0624869818788,0.060383043095,0.0622765880004,0.0622765880004,0.0624869818788,0.0624869818788,0.0616454063653,0.0608038308517,0.0612246186085,0.0626973757572,0.0622765880004,0.0624869818788,0.0597518614598,0.0584894981896,0.0599622553382,0.0612246186085,0.0629077696355,0.0650117084193,0.0650117084193,0.0652221022977,0.0650117084193,0.0637493451491,0.0633285573923,0.064801314541,0.0622765880004,0.0624869818788,0.0629077696355,0.0616454063653,0.0595414675815,0.060383043095,0.0631181635139,0.0666948594464,0.0675364349599,0.0685884043518,0.0704819492572,0.0673260410815,0.0645909206626,0.0629077696355,0.0633285573923,0.0637493451491,0.0629077696355,0.0614350124869,0.0612246186085,0.0601726492166,0.0608038308517,0.062066194122,0.0633285573923,0.0643805267842,0.0645909206626,0.0624869818788,0.0610142247301,0.060383043095,0.0597518614598,0.0586998920679,0.0584894981896,0.0586998920679,0.0584894981896,0.0593310737031,0.0595414675815,0.0601726492166,0.0641701329058,0.0622765880004,0.0622765880004,0.064801314541,0.0652221022977,0.0660636778112,0.0650117084193,0.0635389512707,0.0618558002436,0.0631181635139,0.0597518614598,0.0618558002436,0.0631181635139,0.0614350124869,0.0586998920679,0.0586998920679,0.0578583165544,0.0593310737031,0.0624869818788,0.0586998920679,0.0586998920679,0.0591206798247,0.0599622553382,0.0631181635139,0.064801314541,0.064801314541,0.0666948594464,0.0639597390274,0.064801314541,0.0666948594464,0.0675364349599,0.0687987982302,0.0660636778112,0.0637493451491,0.0637493451491,0.0652221022977,0.0635389512707,0.0652221022977,0.0631181635139,0.0637493451491,0.0635389512707,0.0641701329058,0.0658532839329,0.0656428900545,0.064801314541,0.0637493451491,0.064801314541,0.0683780104734,0.0669052533247,0.0654324961761,0.064801314541,0.0637493451491,0.064801314541,0.0618558002436,0.0641701329058,0.0631181635139,0.0643805267842,0.0624869818788,0.0652221022977,0.0666948594464,0.0671156472031,0.0677468288383,0.0658532839329,0.0675364349599,0.0658532839329,0.0690091921085,0.0677468288383,0.0666948594464,0.066484465568,0.0679572227166,0.068167616595,0.0660636778112,0.0669052533247,0.0671156472031,0.0692195859869,0.0660636778112,0.0677468288383,0.0666948594464,0.0652221022977,0.0658532839329,0.0656428900545,0.0669052533247,0.0671156472031,0.0687987982302,0.0679572227166,0.0698507676221,0.072585888041,0.0767937656086,0.0788977043924,0.0816328248113,0.0845783391086,0.0854199146222,0.0900485799465,0.0919421248519,0.093625275879,0.095308426906,0.09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m <- 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ycorr <- 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altd  <- c(37, 274, 541, 593)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('BCL6_FA_ChIP-seq-GSM2754207-vs-FA_IgG_control-GSM2754209.dedup.pseudoRep2.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) : 37,274,541,593',bty='n')
dev.off()