# R script for Peak Model
#  -- generated by MACS
p <- c(0.0451189872666,0.0526827007819,0.060054927879,0.0677861920101,0.075589263548,0.0760679795933,0.0759004289774,0.0757089425593,0.0757328783616,0.0758764931752,0.0760919153956,0.076044043791,0.0764270166272,0.0761397870001,0.0757089425593,0.0756131993503,0.0754695845367,0.0756850067571,0.0754217129322,0.0753020339209,0.0753977771299,0.0754217129322,0.0750148042937,0.0748951252824,0.0749190610846,0.075038740096,0.0752541623163,0.0754456487344,0.0758764931752,0.0759243647797,0.0760201079888,0.0761637228023,0.0763791450227,0.076857861068,0.0768817968703,0.0765227598363,0.0764748882318,0.0763791450227,0.0763791450227,0.0762355302091,0.0761637228023,0.0761637228023,0.0761876586046,0.0757807499661,0.0760201079888,0.0761158511978,0.0761158511978,0.0759004289774,0.0756131993503,0.0758525573729,0.0757328783616,0.075589263548,0.0756131993503,0.0760679795933,0.0759722363842,0.0761397870001,0.0761876586046,0.0764748882318,0.0766663746499,0.0766424388476,0.0766424388476,0.0766903104521,0.0768339252657,0.0764270166272,0.0766185030454,0.0766185030454,0.0768339252657,0.0765706314408,0.0765945672431,0.0765227598363,0.0765945672431,0.0767621178589,0.0765945672431,0.0765945672431,0.0764270166272,0.076498824034,0.0762115944069,0.076403080825,0.0764748882318,0.0765706314408,0.076498824034,0.0764270166272,0.0765706314408,0.0768099894635,0.0770493474861,0.0768099894635,0.0769296684748,0.0767381820567,0.0769296684748,0.076857861068,0.0769775400793,0.0770014758816,0.0769057326725,0.0767860536612,0.0765466956386,0.0766663746499,0.0765227598363,0.0763073376159,0.0761158511978,0.0761876586046,0.0762355302091,0.0761158511978,0.0760919153956,0.0761876586046,0.0764270166272,0.0762834018137,0.076403080825,0.0767860536612,0.0769775400793,0.0770493474861,0.0769057326725,0.0769775400793,0.0770014758816,0.0770972190906,0.0768339252657,0.0770732832884,0.0770732832884,0.076953604277,0.0770254116838,0.0770014758816,0.0773844487178,0.0775998709382,0.0776716783449,0.0777913573563,0.0780785869834,0.0778152931585,0.0780546511812,0.0783179450061,0.0781982659947,0.0783418808083,0.0780546511812,0.0778631647631,0.0777434857517,0.0774801919268,0.0775519993336,0.0775519993336,0.0774562561246,0.0771690264974,0.0770732832884,0.076857861068,0.0769775400793,0.0772647697065,0.0775759351359,0.0774801919268,0.0774801919268,0.0778152931585,0.0778871005653,0.0781743301925,0.0780546511812,0.0780546511812,0.078126458588,0.077767421554,0.0775759351359,0.0778152931585,0.0777913573563,0.0778871005653,0.0779110363676,0.0777195499495,0.0780067795766,0.0782940092038,0.0784136882151,0.0785573030287,0.078581238831,0.0788445326559,0.0788445326559,0.0788924042604,0.0790120832717,0.0791796338875,0.0790599548762,0.0787009178423,0.0785094314242,0.0782700734015,0.0784136882151,0.0781503943902,0.0782461375993,0.0780307153789,0.0775998709382,0.0775519993336,0.0776238067404,0.0776956141472,0.0777195499495,0.0779589079721,0.0780785869834,0.0780307153789,0.0779110363676,0.078222201797,0.0781503943902,0.0780785869834,0.0780307153789,0.0780546511812,0.0778392289608,0.0778392289608,0.0775759351359,0.0775041277291,0.0776238067404,0.0774323203223,0.0778392289608,0.0777434857517,0.0774323203223,0.0777195499495,0.0777195499495,0.0778871005653,0.0782700734015,0.0783658166106,0.0783418808083,0.0781503943902,0.0779110363676,0.0781025227857,0.0783658166106,0.0782461375993,0.078581238831,0.0785333672264,0.0783179450061,0.0783897524128,0.0783418808083,0.0785573030287,0.0790599548762,0.079131762283,0.0791556980853,0.0792993128989,0.0793711203057,0.0795147351192,0.0797301573396,0.0800652585713,0.0803524881985,0.0806636536279,0.0804242956052,0.080855140046,0.0812620486845,0.0811423696731,0.081405663498,0.0815492783116,0.0818125721365,0.0818604437411,0.0819322511478,0.0820758659614,0.0824827745999,0.0825067104022,0.0827221326225,0.083033298052,0.0830811696565,0.0832487202723,0.0828418116339,0.083129041261,0.0832247844701,0.0832487202723,0.0833444634814,0.0832726560746,0.0833683992836,0.0835359498995,0.0837513721199,0.0838471153289,0.0846609326059,0.0846848684081,0.0848763548262,0.0851875202557,0.0850917770466,0.0852353918602,0.084948162233,0.0849242264308,0.0849960338376,0.0850917770466,0.0847806116172,0.0846848684081,0.084948162233,0.0847806116172,0.084852419024,0.0849002906285,0.0851157128489,0.0852593276625,0.0855226214874,0.085857722719,0.0859295301258,0.0860731449394,0.0857380437077,0.08576197951,0.0858337869168,0.085857722719,0.085857722719,0.0856423004987,0.0854747498828,0.0852114560579,0.0851635844534,0.0851157128489,0.0852353918602,0.0852114560579,0.0851875202557,0.0852593276625,0.085307199267,0.0857141079055,0.0856183646964,0.0856183646964,0.0856183646964,0.0859534659281,0.0860970807417,0.086216759753,0.0864561177756,0.0866236683915,0.0867433474028,0.0869827054254,0.0871981276458,0.0873178066571,0.0877247152956,0.0876050362843,0.0877007794933,0.0878922659114,0.0879162017137,0.087940137516,0.0883470461545,0.088490660968,0.0886821473861,0.0890172486178,0.0890651202224,0.0893762856518,0.0894720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m <- 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ycorr <- 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altd  <- c(3, 208)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('12-AP1-GSE38358/PI-GFP-AP1-GR-ap1-cal-ChIPseq-GSM940585/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) : 3,208',bty='n')
dev.off()