# R script for Peak Model
#  -- generated by MACS
p <- c(0.0482938281928,0.0563213585051,0.0643231595536,0.0723506898659,0.0803524909144,0.0804811372335,0.0806097835526,0.0804554079696,0.0803010323867,0.0804296787058,0.0802753031229,0.0805840542887,0.0806355128164,0.0805840542887,0.0806612420802,0.0807127006079,0.0806612420802,0.0806612420802,0.0805840542887,0.0804554079696,0.0804811372335,0.0801981153314,0.0803524909144,0.0804554079696,0.0803267616505,0.0801981153314,0.0800694690123,0.0799408226932,0.0797349885826,0.0794776959444,0.0791432155147,0.0788601936127,0.078525713183,0.0784227961277,0.0783198790725,0.0781912327534,0.0781912327534,0.0784742546554,0.078525713183,0.0787058180298,0.0788344643489,0.0788344643489,0.0788601936127,0.0788087350851,0.0790402984595,0.0790917569871,0.0792204033062,0.0791689447786,0.0793747788891,0.0793490496253,0.0796063422635,0.0795806129997,0.0797092593188,0.0798893641656,0.0798893641656,0.0799150934294,0.0798636349017,0.0798893641656,0.0798636349017,0.0799922812209,0.079683530055,0.0800180104847,0.0799150934294,0.0797349885826,0.0795548837359,0.0795806129997,0.0793233203615,0.0791689447786,0.0791432155147,0.0789888399318,0.0790402984595,0.0785514424469,0.0781140449619,0.077959669379,0.0776766474769,0.0774450841025,0.0775994596855,0.077522271894,0.0771363329367,0.0768790402985,0.0767246647155,0.0769562280899,0.0772907085196,0.0773164377834,0.0774193548387,0.0775737304216,0.0774450841025,0.0774450841025,0.0774193548387,0.0777281060046,0.0778824815875,0.0777281060046,0.0774965426302,0.0776766474769,0.0779082108513,0.0780883156981,0.078242691281,0.0783456083363,0.0787830058212,0.0786029009745,0.0787315472936,0.0790917569871,0.0792975910977,0.0791174862509,0.0794262374168,0.079400508153,0.0795548837359,0.0796320715274,0.0794776959444,0.0796063422635,0.0795291544721,0.0796320715274,0.0798636349017,0.08012092754,0.0798893641656,0.0797092593188,0.0796578007912,0.0797092593188,0.0798379056379,0.0799150934294,0.0797092593188,0.0796578007912,0.0796063422635,0.0795548837359,0.079683530055,0.0798121763741,0.0800180104847,0.0799150934294,0.079966551957,0.0798121763741,0.0800951982761,0.0800951982761,0.0802495738591,0.0801723860676,0.0798379056379,0.0796578007912,0.079400508153,0.0796320715274,0.0796063422635,0.0798636349017,0.0800694690123,0.0801466568038,0.0801466568038,0.0802753031229,0.0804554079696,0.0806612420802,0.0807641591355,0.0808670761908,0.0810214517737,0.0810471810375,0.0810214517737,0.0808670761908,0.080841346927,0.0810214517737,0.0811758273566,0.0812015566205,0.0814331199949,0.0813816614672,0.0814588492587,0.0817161418969,0.0817161418969,0.0817676004245,0.0814588492587,0.0813816614672,0.0812787444119,0.0812272858843,0.0811758273566,0.0809185347184,0.0809185347184,0.080686971344,0.0805583250249,0.0807127006079,0.0811500980928,0.0809442639822,0.0810214517737,0.0809442639822,0.0807641591355,0.0807641591355,0.0809957225099,0.081124368829,0.0812015566205,0.0812015566205,0.0811758273566,0.0813559322034,0.081407390731,0.081561766314,0.0816389541054,0.0817933296884,0.0813302029396,0.0812272858843,0.081407390731,0.0814588492587,0.0814845785225,0.0813816614672,0.0813302029396,0.0813302029396,0.0811758273566,0.081407390731,0.0816389541054,0.0816646833692,0.0813816614672,0.0812015566205,0.0808928054546,0.081124368829,0.0810214517737,0.080841346927,0.0808670761908,0.0805583250249,0.0803267616505,0.0802753031229,0.080403949442,0.0801466568038,0.0803782201782,0.0800694690123,0.0799408226932,0.0801981153314,0.0803782201782,0.0803524909144,0.0804296787058,0.0806355128164,0.0806355128164,0.0809185347184,0.0808928054546,0.0813559322034,0.0815360370501,0.0814845785225,0.0816646833692,0.0819477052713,0.0818190589522,0.0815874955778,0.0814845785225,0.0811758273566,0.0812015566205,0.0809185347184,0.0808156176631,0.0806612420802,0.0806612420802,0.0803782201782,0.0804554079696,0.0805840542887,0.0806355128164,0.0807384298717,0.080841346927,0.0808670761908,0.081124368829,0.0812272858843,0.0808670761908,0.0812272858843,0.0813816614672,0.0815360370501,0.0815103077863,0.0817676004245,0.0816904126331,0.0817676004245,0.0816904126331,0.0817418711607,0.0817161418969,0.0814845785225,0.0815874955778,0.0812272858843,0.0814331199949,0.0814331199949,0.0815874955778,0.0817161418969,0.0816646833692,0.081844788216,0.0820506223266,0.0818962467436,0.0817161418969,0.0821535393819,0.081844788216,0.0818962467436,0.0816904126331,0.0812530151481,0.0812787444119,0.0809699932461,0.0809185347184,0.0810214517737,0.0810471810375,0.0808156176631,0.080841346927,0.0810214517737,0.0810986395652,0.0814331199949,0.081561766314,0.0818705174798,0.0823079149648,0.0825909368668,0.0829511465603,0.0830283343518,0.0834914611006,0.0833370855176,0.0832598977262,0.0832084391985,0.0834142733091,0.0833628147815,0.0831055221432,0.0830540636156,0.0829254172965,0.0829768758241,0.0825394783392,0.0829254172965,0.0832084391985,0.0834657318367,0.0835171903644,0.0835943781559,0.0835943781559,0.0837487537388,0.0838774000579,0.0838516707941,0.0843662560705,0.0841861512237,0.0840575049046,0.084006046377,0.0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m <- 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ycorr <- 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altd  <- c(0, 29, 57, 104, 207, 432, 465, 510, 529, 568, 591)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('33-SEP3-AP1-24581456/AP1-ChIP-seq-8d-biological-reps-1-and-2-GSM1142628/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) : 0,29,57,104,207,432,465,510,529,568,591',bty='n')
dev.off()