# R script for Peak Model
#  -- generated by MACS
p <- c(0.0511118028948,0.0590290157773,0.067107804433,0.0751327344976,0.0834269575174,0.0829422301981,0.0829422301981,0.0830499473802,0.0825652200608,0.0827267958339,0.0826190786519,0.0832115231533,0.0833730989264,0.0835346746995,0.0835346746995,0.0836962504726,0.0835885332905,0.0830499473802,0.082888371607,0.0829422301981,0.0826729372429,0.0823497856967,0.0825113614698,0.0824575028787,0.0826190786519,0.0826190786519,0.0824575028787,0.0825652200608,0.0825113614698,0.0821882099236,0.0825113614698,0.0824575028787,0.0818650583773,0.0819189169684,0.0818111997863,0.0813264724669,0.0808417451476,0.0807878865566,0.0803031592372,0.0800877248731,0.0799261491,0.0797107147358,0.0800877248731,0.0798184319179,0.0790105530523,0.0790644116434,0.0793875631896,0.0791182702344,0.0796029975537,0.0794414217806,0.0789028358703,0.0787412600971,0.0783642499599,0.0783642499599,0.0779872398226,0.0779333812316,0.0777718054585,0.0782565327778,0.0778795226405,0.0777179468674,0.0781488155957,0.078471967142,0.078579684324,0.0783103913688,0.0789566944613,0.0793337045986,0.0798184319179,0.0793337045986,0.0794414217806,0.0798722905089,0.0800877248731,0.0797645733269,0.0799261491,0.080033866282,0.0798184319179,0.0796029975537,0.0792259874165,0.0790644116434,0.0792259874165,0.0790105530523,0.0787412600971,0.0790644116434,0.0789028358703,0.0790644116434,0.0792259874165,0.0792798460075,0.0793337045986,0.0798722905089,0.0798722905089,0.0797645733269,0.0798184319179,0.0794952803717,0.0797107147358,0.0798184319179,0.0799261491,0.0794952803717,0.0796568561448,0.0790105530523,0.0794414217806,0.0796568561448,0.0794414217806,0.0798722905089,0.0797107147358,0.0796568561448,0.0796029975537,0.0797107147358,0.0791721288254,0.0796029975537,0.0791182702344,0.0792798460075,0.0793337045986,0.0791182702344,0.0789028358703,0.0786335429151,0.0788489772792,0.0790644116434,0.0795491389627,0.0794414217806,0.0798722905089,0.0798184319179,0.0801954420552,0.0808417451476,0.081434189649,0.0815957654221,0.0815957654221,0.0818650583773,0.0820804927415,0.0826729372429,0.0824036442877,0.0820804927415,0.0817573411953,0.0811648966938,0.0810571795118,0.0817034826042,0.0815957654221,0.0815957654221,0.0816496240132,0.0814880482401,0.0818650583773,0.0821882099236,0.0823497856967,0.0827267958339,0.0831576645622,0.0826729372429,0.0829422301981,0.0831038059712,0.0824575028787,0.0820266341504,0.0816496240132,0.0813264724669,0.0812726138759,0.0808417451476,0.0801415834641,0.0801954420552,0.0802493006462,0.079980007691,0.0806263107835,0.0806263107835,0.0810033209207,0.081434189649,0.0816496240132,0.0817573411953,0.0821882099236,0.0824036442877,0.0820266341504,0.0821343513325,0.0817034826042,0.0819189169684,0.0812187552849,0.0808417451476,0.0802493006462,0.0802493006462,0.079980007691,0.0799261491,0.079980007691,0.0798184319179,0.0800877248731,0.0796029975537,0.0802493006462,0.0805185936014,0.0807340279655,0.0806263107835,0.0804108764193,0.0803031592372,0.0804108764193,0.0804108764193,0.0798722905089,0.0801954420552,0.0798184319179,0.0798722905089,0.0797645733269,0.0799261491,0.079980007691,0.0800877248731,0.080033866282,0.080033866282,0.0804647350103,0.0801954420552,0.0800877248731,0.0798722905089,0.0797107147358,0.0794414217806,0.0795491389627,0.0791721288254,0.0792798460075,0.0791721288254,0.078471967142,0.0786335429151,0.0787951186882,0.0783642499599,0.0786335429151,0.0783103913688,0.0783103913688,0.0781488155957,0.0773409367302,0.0773947953212,0.0778256640495,0.0775563710943,0.0769639265929,0.0776102296853,0.0775563710943,0.0780410984136,0.0775563710943,0.0777179468674,0.0783642499599,0.0780949570047,0.0783103913688,0.0782565327778,0.0786335429151,0.078525825733,0.0786335429151,0.0783642499599,0.0788489772792,0.0786335429151,0.0789566944613,0.0792259874165,0.0790644116434,0.0793875631896,0.0796029975537,0.0796568561448,0.0796029975537,0.0801415834641,0.079980007691,0.0805724521924,0.0800877248731,0.080033866282,0.0800877248731,0.079980007691,0.0796568561448,0.0794414217806,0.0791721288254,0.078579684324,0.078471967142,0.0779872398226,0.0779872398226,0.0780410984136,0.0778256640495,0.0778795226405,0.0782565327778,0.0784181085509,0.0787412600971,0.0790644116434,0.0791721288254,0.0796568561448,0.0800877248731,0.0801954420552,0.0807340279655,0.0810033209207,0.0812726138759,0.081380331058,0.081380331058,0.0815419068311,0.081434189649,0.0813264724669,0.0812726138759,0.0815419068311,0.0817573411953,0.0819189169684,0.0818650583773,0.0820266341504,0.0825652200608,0.0826729372429,0.0825652200608,0.0824575028787,0.0821343513325,0.0820266341504,0.0815957654221,0.0810571795118,0.0812726138759,0.0814880482401,0.0813264724669,0.0812726138759,0.0813264724669,0.0815419068311,0.0819727755594,0.0819727755594,0.0817573411953,0.0826190786519,0.0819189169684,0.0815419068311,0.0812187552849,0.0808417451476,0.0808956037386,0.0805724521924,0.0807878865566,0.0802493006462,0.0804647350103,0.0799261491,0.0801954420552,0.0801415834641,0.0805724521924,0.0811110381028,0.0814880482401,0.0817573411953,0.0812187552849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m <- 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ycorr <- 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altd  <- c(1, 38, 101, 125, 185, 238, 259, 408, 428, 453, 474, 555)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('59-RGA-GSE59187/RGA_ChIP3-GSM1429899/all.1x36mers.TAIR10.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) : 1,38,101,125,185,238,259,408,428,453,474,555',bty='n')
dev.off()