# R script for Peak Model
#  -- generated by MACS
p <- c(0.0459539192803,0.053642882291,0.0618264569573,0.0692456317922,0.0774292064585,0.0770694888908,0.0765748772351,0.0763050890593,0.0764399831472,0.076754736019,0.0759903361875,0.0749561481803,0.0746413953085,0.0742816777407,0.0732924544294,0.0734273485173,0.0734273485173,0.0730676309496,0.0731575603415,0.0727079133818,0.0729777015576,0.0732924544294,0.0727528780778,0.0723032311181,0.0725280545979,0.0718086194624,0.0718086194624,0.07239316051,0.0727079133818,0.0726629486858,0.0728428074697,0.0732924544294,0.0735172779092,0.073832030781,0.0736971366931,0.073921960173,0.0733823838213,0.0730676309496,0.0727978427737,0.0731125956455,0.0728428074697,0.0723032311181,0.0718985488544,0.0720334429423,0.07239316051,0.0720784076382,0.0723481958141,0.0715837959826,0.0718985488544,0.0706845020632,0.0705496079753,0.0711791137189,0.0715837959826,0.0719435135503,0.0714489018947,0.0723032311181,0.072438125206,0.0736971366931,0.0731575603415,0.0740568542609,0.0745514659165,0.0737870660851,0.0730676309496,0.0728877721657,0.07239316051,0.0714938665906,0.0713140078068,0.0708643608471,0.070909325543,0.0703247844955,0.0703247844955,0.0704147138874,0.0704596785834,0.0702798197995,0.0706395373672,0.0706395373672,0.0706845020632,0.0701449257116,0.0700999610156,0.0713140078068,0.0707294667592,0.0708643608471,0.0714938665906,0.0716737253745,0.0714938665906,0.0714039371987,0.0705496079753,0.0707294667592,0.0708193961511,0.0699650669277,0.06960534936,0.06960534936,0.0691557024003,0.0689758436164,0.0684362672648,0.0679416556091,0.0686610907446,0.0694254905761,0.0691557024003,0.06960534936,0.0700999610156,0.0703247844955,0.0705945726713,0.0707744314551,0.0719884782463,0.0728428074697,0.0730226662536,0.0728428074697,0.0736521719972,0.0733823838213,0.0741917483488,0.0743266424367,0.0744165718286,0.0741018189568,0.0737421013891,0.0742367130448,0.0745065012206,0.0741467836528,0.0730226662536,0.0729327368617,0.072483089902,0.0726179839899,0.0722582664221,0.0722582664221,0.0730676309496,0.0727079133818,0.0727978427737,0.0723481958141,0.0728428074697,0.0733374191254,0.0727528780778,0.0718535841584,0.0720334429423,0.0727528780778,0.0721233723342,0.0719884782463,0.0716737253745,0.0717186900705,0.0715837959826,0.070909325543,0.0714938665906,0.0723032311181,0.0720334429423,0.0712240784148,0.0708193961511,0.0704147138874,0.0701898904075,0.0701449257116,0.0702348551035,0.0715837959826,0.0720334429423,0.072483089902,0.0731125956455,0.0731575603415,0.0733823838213,0.0741018189568,0.0741917483488,0.0745065012206,0.0747762893964,0.0742816777407,0.0732474897334,0.0725730192939,0.0723032311181,0.0727978427737,0.0726179839899,0.0714489018947,0.0717186900705,0.0716287606786,0.0715388312866,0.0718086194624,0.0727528780778,0.0733374191254,0.0742367130448,0.0748662187883,0.0756306186198,0.076799700715,0.0769795594989,0.0772043829787,0.076754736019,0.0759903361875,0.0755406892279,0.0754957245319,0.0754057951399,0.0751809716601,0.075270901052,0.0750910422682,0.0752259363561,0.0749561481803,0.075270901052,0.0752259363561,0.0761252302754,0.0754057951399,0.075315865748,0.0749111834843,0.0749111834843,0.0749561481803,0.0745065012206,0.0750910422682,0.0756306186198,0.0759903361875,0.0759004067956,0.0759004067956,0.0750910422682,0.0749111834843,0.0745964306125,0.0747313247004,0.0745065012206,0.0743266424367,0.0741018189568,0.0735172779092,0.0732474897334,0.0742816777407,0.0745514659165,0.0755856539238,0.0759004067956,0.0759453714916,0.0764399831472,0.0766198419311,0.076754736019,0.0774292064585,0.0770245241948,0.0765299125392,0.0765299125392,0.0764399831472,0.0764849478432,0.0765748772351,0.0769795594989,0.0766198419311,0.0764399831472,0.0766648066271,0.0773392770666,0.0781486415941,0.0789580061215,0.07819360629,0.078283535682,0.0781486415941,0.0784633944658,0.079632476561,0.0799921941288,0.0802619823046,0.0799472294328,0.0802619823046,0.079722405953,0.0800371588247,0.0798573000409,0.0807116292643,0.0800821235207,0.0798573000409,0.0803968763925,0.0806216998723,0.0808465233522,0.0800821235207,0.0804418410885,0.081116311528,0.0813860997038,0.0808465233522,0.0818807113595,0.0822853936232,0.0820156054474,0.0818357466635,0.0820156054474,0.0823303583192,0.082600146495,0.0821954642313,0.0824202877111,0.082555181799,0.0824202877111,0.0821954642313,0.0828249699748,0.0830497934547,0.0830497934547,0.0826451111909,0.0817458172716,0.0817458172716,0.0817008525756,0.0819256760554,0.0812512056159,0.0805317704804,0.0803968763925,0.0801270882167,0.079632476561,0.0798573000409,0.0807565939603,0.0802170176086,0.0803519116965,0.0804418410885,0.081161276224,0.0812961703119,0.0808914880482,0.0814760290958,0.0818807113595,0.0824202877111,0.082555181799,0.0839041226781,0.0837692285902,0.0850282400773,0.0844886637257,0.0849383106854,0.085432922341,0.0851181694692,0.0857476752128,0.0860174633886,0.0857476752128,0.085522851733,0.0857476752128,0.0850282400773,0.0853429929491,0.0858376046047,0.0860174633886,0.0862422868685,0.0862872515644,0.0870516513959,0.0874563336596,0.0882656981871,0.088850239234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m <- 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ycorr <- 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altd  <- c(4, 223)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('21-AMS-GSE16940/AMS_ChIPSeq-GSM424618/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) : 4,223',bty='n')
dev.off()